I: pbuilder: network access will be disabled during build I: Current time: Sun Mar 13 08:16:38 -12 2022 I: pbuilder-time-stamp: 1647202598 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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_2019.1-1.dsc] I: copying [./gromacs_2019.1.orig.tar.gz] I: copying [./gromacs_2019.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Feb 17 06:12:37 2019 -12 gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F gpgv: issuer "nbreen@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gromacs_2019.1-1.dsc dpkg-source: info: extracting gromacs in gromacs-2019.1 dpkg-source: info: unpacking gromacs_2019.1.orig.tar.gz dpkg-source: info: unpacking gromacs_2019.1-1.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 doxygen.patch dpkg-source: info: applying disable-cpuinfotest.patch dpkg-source: info: applying mdrun-test-timeout.patch dpkg-source: info: applying local-mathjax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2947/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='2947' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.T0KpgIs1jP/pbuilderrc_zTfA --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.T0KpgIs1jP/b1 --logfile b1/build.log gromacs_2019.1-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink13-arm64 4.15.0-135-generic #139-Ubuntu SMP Mon Jan 18 17:40:29 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Mar 12 02:48 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/2947/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: chrpath, cmake, debhelper (>= 11), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.10.2-7), libx11-dev, mpich, openmpi-bin, zlib1g-dev, doxygen, ghostscript, graphviz, imagemagick, mscgen, python-sphinx (>= 1.4.1), rdfind, symlinks, 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 ... 19168 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 chrpath; however: Package chrpath is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper (>= 11); however: Package debhelper 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 liblapack-dev; however: Package liblapack-dev is not installed. pbuilder-satisfydepends-dummy depends on libmpich-dev (>= 3.0.4-6); however: Package libmpich-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmpi-dev (>= 1.10.2-7); however: Package libopenmpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libx11-dev; however: Package libx11-dev is not installed. pbuilder-satisfydepends-dummy depends on mpich; however: Package mpich is not installed. pbuilder-satisfydepends-dummy depends on openmpi-bin; however: Package openmpi-bin 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 graphviz; however: Package graphviz is not installed. pbuilder-satisfydepends-dummy depends on imagemagick; however: Package imagemagick is not installed. pbuilder-satisfydepends-dummy depends on mscgen; however: Package mscgen is not installed. pbuilder-satisfydepends-dummy depends on python-sphinx (>= 1.4.1); however: Package python-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 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} bsdmainutils{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-dejavu-core{a} fonts-lmodern{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} ghostscript{a} graphviz{a} groff-base{a} hicolor-icon-theme{a} hwloc-nox{a} ibverbs-providers{a} imagemagick{a} imagemagick-6-common{a} imagemagick-6.q16{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas-dev{a} libblas3{a} libboost-dev{a} libboost1.67-dev{a} libbrotli1{a} libbsd0{a} libcairo2{a} libcdt5{a} libcgraph6{a} libclang1-6.0{a} libcroco3{a} libcups2{a} libcupsimage2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libde265-0{a} libedit2{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-single3{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgd3{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgraphite2-3{a} libgs9{a} libgs9-common{a} libgssapi-krb5-2{a} libgts-0.7-5{a} libgvc6{a} libgvpr2{a} libharfbuzz-icu0{a} libharfbuzz0b{a} libheif1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu63{a} libidn11{a} libijs-0.35{a} libjbig0{a} libjbig2dec0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkpathsea6{a} libkrb5-3{a} libkrb5support0{a} liblab-gamut1{a} liblapack-dev{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} libldap-common{a} libllvm6.0{a} liblqr-1-0{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmagickcore-6.q16-6{a} libmagickwand-6.q16-6{a} libmpich-dev{a} libmpich12{a} libncurses6{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} libpipeline1{a} libpixman-1-0{a} libpmix2{a} libpng16-16{a} libpotrace0{a} libprocps7{a} libpsl5{a} libptexenc1{a} libpthread-stubs0-dev{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsm6{a} libssh2-1{a} libssl1.1{a} libsynctex2{a} libteckit0{a} libtexlua52{a} libtexlua53{a} libthai-data{a} libthai0{a} libtiff5{a} libtool{a} libuchardet0{a} libuv1{a} libwebp6{a} libwebpmux3{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx265-165{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxdot4{a} libxext6{a} libxi6{a} libxml2{a} libxmu6{a} libxpm4{a} libxrender1{a} libxt6{a} libxxhash0{a} libzzip-0-13{a} lsb-base{a} m4{a} man-db{a} mime-support{a} mpich{a} mscgen{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} po-debconf{a} poppler-data{a} preview-latex-style{a} procps{a} python{a} python-alabaster{a} python-babel{a} python-babel-localedata{a} python-certifi{a} python-chardet{a} python-docutils{a} python-idna{a} python-imagesize{a} python-jinja2{a} python-markupsafe{a} python-minimal{a} python-packaging{a} python-pkg-resources{a} python-pygments{a} python-pyparsing{a} python-requests{a} python-roman{a} python-six{a} python-sphinx{a} python-typing{a} python-tz{a} python-urllib3{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} rdfind{a} readline-common{a} sensible-utils{a} sgml-base{a} sphinx-common{a} symlinks{a} t1utils{a} tex-common{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} ucf{a} x11-common{a} x11proto-core-dev{a} x11proto-dev{a} xdg-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 docutils-doc fonts-droid-fallback fonts-liberation gsfonts javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libcupsfilters1 libfile-mimeinfo-perl libglib2.0-data libgpm2 libgts-bin libmagickcore-6.q16-6-extra libmail-sendmail-perl libnet-dbus-perl libsasl2-modules libx11-protocol-perl lmodern lynx netpbm psmisc publicsuffix python-cryptography python-enum34 python-ipaddress python-openssl python-pil ruby shared-mime-info tex-gyre texlive-plain-generic tipa tk wget x11-utils x11-xserver-utils xauth xdg-user-dirs 0 packages upgraded, 264 newly installed, 0 to remove and 0 not upgraded. Need to get 200 MB of archives. After unpacking 841 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u4 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 libfftw3-double3 arm64 3.3.8-2 [385 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libpng16-16 arm64 1.6.36-6 [287 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libfreetype6 arm64 2.9.1-3+deb10u2 [355 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 ucf all 3.0038+nmu1 [69.0 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 fonts-dejavu-core all 2.37-1 [1068 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 fontconfig-config all 2.13.1-2 [280 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 libfontconfig1 arm64 2.13.1-2 [343 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 libde265-0 arm64 1.0.3-1+b1 [205 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 libnuma1 arm64 2.0.12-1 [25.6 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 libx265-165 arm64 2.9-4 [536 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 libheif1 arm64 1.3.2-2~deb10u1 [114 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libjpeg62-turbo arm64 1:1.5.2-2+deb10u1 [123 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 liblcms2-2 arm64 2.9-3 [137 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 liblqr-1-0 arm64 0.4.2-2.1 [23.9 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 libltdl7 arm64 2.4.6-9 [389 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 libopenjp2-7 arm64 2.3.0-2+deb10u1 [148 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 libwebp6 arm64 0.6.1-2 [233 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libtiff5 arm64 4.1.0+git191117-2~deb10u1 [259 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 libwebpmux3 arm64 0.6.1-2 [95.4 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libxau6 arm64 1:1.0.8-1+b2 [19.3 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 libxcb1 arm64 1.13.1-2 [135 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libx11-data all 2:1.6.7-1+deb10u1 [294 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 libx11-6 arm64 2:1.6.7-1+deb10u1 [734 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libxext6 arm64 2:1.3.3-1+b2 [48.6 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+deb10u1 [625 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 imagemagick-6-common all 8:6.9.10.23+dfsg-2.1+deb10u1 [200 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libmagickcore-6.q16-6 arm64 8:6.9.10.23+dfsg-2.1+deb10u1 [1594 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 libmagickwand-6.q16-6 arm64 8:6.9.10.23+dfsg-2.1+deb10u1 [387 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 poppler-data all 0.4.9-2 [1473 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 sgml-base all 1.29 [14.8 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 tex-common all 6.11 [53.1 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 59 http://deb.debian.org/debian buster/main arm64 libprocps7 arm64 2:3.3.15-2 [58.0 kB] Get: 60 http://deb.debian.org/debian buster/main arm64 lsb-base all 10.2019051400 [28.4 kB] Get: 61 http://deb.debian.org/debian buster/main arm64 procps arm64 2:3.3.15-2 [245 kB] Get: 62 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u2 [242 kB] Get: 63 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u2 [115 kB] Get: 64 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u2 [66.5 kB] Get: 65 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 66 http://deb.debian.org/debian buster/main arm64 libedit2 arm64 3.1-20181209-1 [91.2 kB] Get: 67 http://deb.debian.org/debian buster/main arm64 libkeyutils1 arm64 1.6-6 [14.9 kB] Get: 68 http://deb.debian.org/debian buster/main arm64 libkrb5support0 arm64 1.17-3+deb10u1 [64.9 kB] Get: 69 http://deb.debian.org/debian buster/main arm64 libk5crypto3 arm64 1.17-3+deb10u1 [123 kB] Get: 70 http://deb.debian.org/debian buster/main arm64 libkrb5-3 arm64 1.17-3+deb10u1 [351 kB] Get: 71 http://deb.debian.org/debian buster/main arm64 libgssapi-krb5-2 arm64 1.17-3+deb10u1 [150 kB] Get: 72 http://deb.debian.org/debian buster/main arm64 openssh-client arm64 1:7.9p1-10+deb10u2 [757 kB] Get: 73 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 74 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 75 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 76 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 77 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 78 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 79 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u4 [823 kB] Get: 80 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20200601~deb10u2 [166 kB] Get: 81 http://deb.debian.org/debian buster/main arm64 chrpath arm64 0.16-2+b1 [16.0 kB] Get: 82 http://deb.debian.org/debian buster/main arm64 cmake-data all 3.13.4-1 [1476 kB] Get: 83 http://deb.debian.org/debian buster/main arm64 libarchive13 arm64 3.3.3-4+deb10u1 [291 kB] Get: 84 http://deb.debian.org/debian buster/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-1+deb10u1 [69.3 kB] Get: 85 http://deb.debian.org/debian buster/main arm64 libsasl2-2 arm64 2.1.27+dfsg-1+deb10u1 [105 kB] Get: 86 http://deb.debian.org/debian buster/main arm64 libldap-common all 2.4.47+dfsg-3+deb10u4 [89.8 kB] Get: 87 http://deb.debian.org/debian buster/main arm64 libldap-2.4-2 arm64 2.4.47+dfsg-3+deb10u4 [216 kB] Get: 88 http://deb.debian.org/debian buster/main arm64 libnghttp2-14 arm64 1.36.0-2+deb10u1 [81.9 kB] Get: 89 http://deb.debian.org/debian buster/main arm64 libpsl5 arm64 0.20.2-2 [53.6 kB] Get: 90 http://deb.debian.org/debian buster/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2 [55.7 kB] Get: 91 http://deb.debian.org/debian buster/main arm64 libssh2-1 arm64 1.8.0-2.1 [135 kB] Get: 92 http://deb.debian.org/debian buster/main arm64 libcurl4 arm64 7.64.0-4+deb10u1 [312 kB] Get: 93 http://deb.debian.org/debian buster/main arm64 libjsoncpp1 arm64 1.7.4-3 [71.0 kB] Get: 94 http://deb.debian.org/debian buster/main arm64 librhash0 arm64 1.3.8-1 [121 kB] Get: 95 http://deb.debian.org/debian buster/main arm64 libuv1 arm64 1.24.1-1 [105 kB] Get: 96 http://deb.debian.org/debian buster/main arm64 cmake arm64 3.13.4-1 [3046 kB] Get: 97 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 98 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 99 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 100 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 101 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 102 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 103 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 104 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 105 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 106 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 107 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 108 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 109 http://deb.debian.org/debian buster/main arm64 xml-core all 0.18+nmu1 [23.8 kB] Get: 110 http://deb.debian.org/debian buster/main arm64 docutils-common all 0.14+dfsg-4 [167 kB] Get: 111 http://deb.debian.org/debian buster/main arm64 libllvm6.0 arm64 1:6.0.1-10 [13.1 MB] Get: 112 http://deb.debian.org/debian buster/main arm64 libclang1-6.0 arm64 1:6.0.1-10 [6190 kB] Get: 113 http://deb.debian.org/debian buster/main arm64 doxygen arm64 1.8.13-10 [3701 kB] Get: 114 http://deb.debian.org/debian buster/main arm64 fontconfig arm64 2.13.1-2 [405 kB] Get: 115 http://deb.debian.org/debian buster/main arm64 fonts-lmodern all 2.004.5-6 [4539 kB] Get: 116 http://deb.debian.org/debian buster/main arm64 libgfortran5 arm64 8.3.0-6 [298 kB] Get: 117 http://deb.debian.org/debian buster/main arm64 libgfortran-8-dev arm64 8.3.0-6 [346 kB] Get: 118 http://deb.debian.org/debian buster/main arm64 gfortran-8 arm64 8.3.0-6 [7861 kB] Get: 119 http://deb.debian.org/debian buster/main arm64 gfortran arm64 4:8.3.0-1 [1420 B] Get: 120 http://deb.debian.org/debian buster/main arm64 libgs9-common all 9.27~dfsg-2+deb10u4 [5136 kB] Get: 121 http://deb.debian.org/debian buster/main arm64 libavahi-common-data arm64 0.7-4+b1 [122 kB] Get: 122 http://deb.debian.org/debian buster/main arm64 libavahi-common3 arm64 0.7-4+b1 [53.5 kB] Get: 123 http://deb.debian.org/debian buster/main arm64 libdbus-1-3 arm64 1.12.20-0+deb10u1 [206 kB] Get: 124 http://deb.debian.org/debian buster/main arm64 libavahi-client3 arm64 0.7-4+b1 [56.8 kB] Get: 125 http://deb.debian.org/debian buster/main arm64 libcups2 arm64 2.2.10-6+deb10u4 [310 kB] Get: 126 http://deb.debian.org/debian buster/main arm64 libcupsimage2 arm64 2.2.10-6+deb10u4 [132 kB] Get: 127 http://deb.debian.org/debian buster/main arm64 libidn11 arm64 1.33-2.2 [113 kB] Get: 128 http://deb.debian.org/debian buster/main arm64 libijs-0.35 arm64 0.35-14 [17.9 kB] Get: 129 http://deb.debian.org/debian buster/main arm64 libjbig2dec0 arm64 0.16-1 [58.1 kB] Get: 130 http://deb.debian.org/debian buster/main arm64 libpaper1 arm64 1.1.28 [21.1 kB] Get: 131 http://deb.debian.org/debian buster/main arm64 libgs9 arm64 9.27~dfsg-2+deb10u4 [2027 kB] Get: 132 http://deb.debian.org/debian buster/main arm64 ghostscript arm64 9.27~dfsg-2+deb10u4 [95.0 kB] Get: 133 http://deb.debian.org/debian buster/main arm64 libpixman-1-0 arm64 0.36.0-1 [436 kB] Get: 134 http://deb.debian.org/debian buster/main arm64 libxcb-render0 arm64 1.13.1-2 [108 kB] Get: 135 http://deb.debian.org/debian buster/main arm64 libxcb-shm0 arm64 1.13.1-2 [99.3 kB] Get: 136 http://deb.debian.org/debian buster/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 137 http://deb.debian.org/debian buster/main arm64 libcairo2 arm64 1.16.0-4+deb10u1 [644 kB] Get: 138 http://deb.debian.org/debian buster/main arm64 libcdt5 arm64 2.40.1-6 [59.6 kB] Get: 139 http://deb.debian.org/debian buster/main arm64 libcgraph6 arm64 2.40.1-6 [81.8 kB] Get: 140 http://deb.debian.org/debian buster/main arm64 libxpm4 arm64 1:3.5.12-1 [43.9 kB] Get: 141 http://deb.debian.org/debian buster/main arm64 libgd3 arm64 2.2.5-5.2 [125 kB] Get: 142 http://deb.debian.org/debian buster/main arm64 libgts-0.7-5 arm64 0.7.6+darcs121130-4 [125 kB] Get: 143 http://deb.debian.org/debian buster/main arm64 libfribidi0 arm64 1.0.5-3.1+deb10u1 [63.6 kB] Get: 144 http://deb.debian.org/debian buster/main arm64 libthai-data all 0.1.28-2 [170 kB] Get: 145 http://deb.debian.org/debian buster/main arm64 libdatrie1 arm64 0.2.12-2 [38.6 kB] Get: 146 http://deb.debian.org/debian buster/main arm64 libthai0 arm64 0.1.28-2 [52.8 kB] Get: 147 http://deb.debian.org/debian buster/main arm64 libpango-1.0-0 arm64 1.42.4-8~deb10u1 [179 kB] Get: 148 http://deb.debian.org/debian buster/main arm64 libgraphite2-3 arm64 1.3.13-7 [75.8 kB] Get: 149 http://deb.debian.org/debian buster/main arm64 libharfbuzz0b arm64 2.3.1-1 [1155 kB] Get: 150 http://deb.debian.org/debian buster/main arm64 libpangoft2-1.0-0 arm64 1.42.4-8~deb10u1 [65.7 kB] Get: 151 http://deb.debian.org/debian buster/main arm64 libpangocairo-1.0-0 arm64 1.42.4-8~deb10u1 [54.0 kB] Get: 152 http://deb.debian.org/debian buster/main arm64 libpathplan4 arm64 2.40.1-6 [61.9 kB] Get: 153 http://deb.debian.org/debian buster/main arm64 libxdot4 arm64 2.40.1-6 [57.0 kB] Get: 154 http://deb.debian.org/debian buster/main arm64 libgvc6 arm64 2.40.1-6 [590 kB] Get: 155 http://deb.debian.org/debian buster/main arm64 libgvpr2 arm64 2.40.1-6 [204 kB] Get: 156 http://deb.debian.org/debian buster/main arm64 x11-common all 1:7.7+19 [251 kB] Get: 157 http://deb.debian.org/debian buster/main arm64 libice6 arm64 2:1.0.9-2 [52.0 kB] Get: 158 http://deb.debian.org/debian buster/main arm64 liblab-gamut1 arm64 2.40.1-6 [220 kB] Get: 159 http://deb.debian.org/debian buster/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 160 http://deb.debian.org/debian buster/main arm64 libxt6 arm64 1:1.1.5-1+b3 [175 kB] Get: 161 http://deb.debian.org/debian buster/main arm64 libxmu6 arm64 2:1.1.2-2+b3 [57.8 kB] Get: 162 http://deb.debian.org/debian buster/main arm64 libxaw7 arm64 2:1.0.13-1+b2 [167 kB] Get: 163 http://deb.debian.org/debian buster/main arm64 graphviz arm64 2.40.1-6 [560 kB] Get: 164 http://deb.debian.org/debian buster/main arm64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get: 165 http://deb.debian.org/debian buster/main arm64 libhwloc5 arm64 1.11.12-3 [97.9 kB] Get: 166 http://deb.debian.org/debian buster/main arm64 hwloc-nox arm64 1.11.12-3 [151 kB] Get: 167 http://deb.debian.org/debian buster/main arm64 libnl-3-200 arm64 3.4.0-1 [54.9 kB] Get: 168 http://deb.debian.org/debian buster/main arm64 libnl-route-3-200 arm64 3.4.0-1 [134 kB] Get: 169 http://deb.debian.org/debian buster/main arm64 libibverbs1 arm64 22.1-1 [47.8 kB] Get: 170 http://deb.debian.org/debian buster/main arm64 ibverbs-providers arm64 22.1-1 [174 kB] Get: 171 http://deb.debian.org/debian buster/main arm64 imagemagick-6.q16 arm64 8:6.9.10.23+dfsg-2.1+deb10u1 [580 kB] Get: 172 http://deb.debian.org/debian buster/main arm64 imagemagick arm64 8:6.9.10.23+dfsg-2.1+deb10u1 [156 kB] Get: 173 http://deb.debian.org/debian buster/main arm64 libblas3 arm64 3.8.0-2 [100 kB] Get: 174 http://deb.debian.org/debian buster/main arm64 libblas-dev arm64 3.8.0-2 [105 kB] Get: 175 http://deb.debian.org/debian buster/main arm64 libboost1.67-dev arm64 1.67.0-13+deb10u1 [8388 kB] Get: 176 http://deb.debian.org/debian buster/main arm64 libboost-dev arm64 1.67.0.1 [3864 B] Get: 177 http://deb.debian.org/debian buster/main arm64 libbrotli1 arm64 1.0.7-2+deb10u1 [262 kB] Get: 178 http://deb.debian.org/debian buster/main arm64 libevent-2.1-6 arm64 2.1.8-stable-4 [150 kB] Get: 179 http://deb.debian.org/debian buster/main arm64 libevent-core-2.1-6 arm64 2.1.8-stable-4 [112 kB] Get: 180 http://deb.debian.org/debian buster/main arm64 libevent-pthreads-2.1-6 arm64 2.1.8-stable-4 [47.7 kB] Get: 181 http://deb.debian.org/debian buster/main arm64 libfftw3-long3 arm64 3.3.8-2 [526 kB] Get: 182 http://deb.debian.org/debian buster/main arm64 libfftw3-single3 arm64 3.3.8-2 [630 kB] Get: 183 http://deb.debian.org/debian buster/main arm64 libfftw3-bin arm64 3.3.8-2 [47.4 kB] Get: 184 http://deb.debian.org/debian buster/main arm64 libfftw3-dev arm64 3.3.8-2 [1455 kB] Get: 185 http://deb.debian.org/debian buster/main arm64 libharfbuzz-icu0 arm64 2.3.1-1 [834 kB] Get: 186 http://deb.debian.org/debian buster/main arm64 libnuma-dev arm64 2.0.12-1 [40.0 kB] Get: 187 http://deb.debian.org/debian buster/main arm64 libltdl-dev arm64 2.4.6-9 [162 kB] Get: 188 http://deb.debian.org/debian buster/main arm64 libhwloc-dev arm64 1.11.12-3 [165 kB] Get: 189 http://deb.debian.org/debian buster/main arm64 libpciaccess0 arm64 0.14-1 [51.0 kB] Get: 190 http://deb.debian.org/debian buster/main arm64 ocl-icd-libopencl1 arm64 2.2.12-2 [37.4 kB] Get: 191 http://deb.debian.org/debian buster/main arm64 libhwloc-plugins arm64 1.11.12-3 [16.9 kB] Get: 192 http://deb.debian.org/debian buster/main arm64 libnl-3-dev arm64 3.4.0-1 [98.2 kB] Get: 193 http://deb.debian.org/debian buster/main arm64 libnl-route-3-dev arm64 3.4.0-1 [162 kB] Get: 194 http://deb.debian.org/debian buster/main arm64 libibverbs-dev arm64 22.1-1 [356 kB] Get: 195 http://deb.debian.org/debian buster/main arm64 libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 196 http://deb.debian.org/debian buster/main arm64 libjs-underscore all 1.9.1~dfsg-1 [99.4 kB] Get: 197 http://deb.debian.org/debian buster/main arm64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get: 198 http://deb.debian.org/debian buster/main arm64 libkpathsea6 arm64 2018.20181218.49446-1 [164 kB] Get: 199 http://deb.debian.org/debian buster/main arm64 liblapack3 arm64 3.8.0-2 [1489 kB] Get: 200 http://deb.debian.org/debian buster/main arm64 liblapack-dev arm64 3.8.0-2 [1524 kB] Get: 201 http://deb.debian.org/debian buster/main arm64 libmpich12 arm64 3.3-3 [994 kB] Get: 202 http://deb.debian.org/debian buster/main arm64 mpich arm64 3.3-3 [361 kB] Get: 203 http://deb.debian.org/debian buster/main arm64 libmpich-dev arm64 3.3-3 [1351 kB] Get: 204 http://deb.debian.org/debian buster/main arm64 libpmix2 arm64 3.1.2-3 [455 kB] Get: 205 http://deb.debian.org/debian buster/main arm64 libopenmpi3 arm64 3.1.3-11 [1996 kB] Get: 206 http://deb.debian.org/debian buster/main arm64 openmpi-common all 3.1.3-11 [165 kB] Get: 207 http://deb.debian.org/debian buster/main arm64 openmpi-bin arm64 3.1.3-11 [199 kB] Get: 208 http://deb.debian.org/debian buster/main arm64 libopenmpi-dev arm64 3.1.3-11 [974 kB] Get: 209 http://deb.debian.org/debian buster/main arm64 libpaper-utils arm64 1.1.28 [18.0 kB] Get: 210 http://deb.debian.org/debian buster/main arm64 libpotrace0 arm64 1.15-1 [23.6 kB] Get: 211 http://deb.debian.org/debian buster/main arm64 libptexenc1 arm64 2018.20181218.49446-1 [60.3 kB] Get: 212 http://deb.debian.org/debian buster/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get: 213 http://deb.debian.org/debian buster/main arm64 libsynctex2 arm64 2018.20181218.49446-1 [77.8 kB] Get: 214 http://deb.debian.org/debian buster/main arm64 libteckit0 arm64 2.5.8+ds2-5 [284 kB] Get: 215 http://deb.debian.org/debian buster/main arm64 libtexlua52 arm64 2018.20181218.49446-1 [107 kB] Get: 216 http://deb.debian.org/debian buster/main arm64 libtexlua53 arm64 2018.20181218.49446-1 [118 kB] Get: 217 http://deb.debian.org/debian buster/main arm64 libwoff1 arm64 1.0.2-1 [40.7 kB] Get: 218 http://deb.debian.org/debian buster/main arm64 xorg-sgml-doctools all 1:1.11-1 [21.9 kB] Get: 219 http://deb.debian.org/debian buster/main arm64 x11proto-dev all 2018.4-4 [251 kB] Get: 220 http://deb.debian.org/debian buster/main arm64 x11proto-core-dev all 2018.4-4 [3128 B] Get: 221 http://deb.debian.org/debian buster/main arm64 libxau-dev arm64 1:1.0.8-1+b2 [22.8 kB] Get: 222 http://deb.debian.org/debian buster/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get: 223 http://deb.debian.org/debian buster/main arm64 xtrans-dev all 1.3.5-1 [100 kB] Get: 224 http://deb.debian.org/debian buster/main arm64 libxcb1-dev arm64 1.13.1-2 [174 kB] Get: 225 http://deb.debian.org/debian buster/main arm64 libx11-dev arm64 2:1.6.7-1+deb10u1 [811 kB] Get: 226 http://deb.debian.org/debian buster/main arm64 libxi6 arm64 2:1.7.9-1 [79.0 kB] Get: 227 http://deb.debian.org/debian buster/main arm64 libxxhash0 arm64 0.6.5-2 [7684 B] Get: 228 http://deb.debian.org/debian buster/main arm64 libzzip-0-13 arm64 0.13.62-3.2 [55.5 kB] Get: 229 http://deb.debian.org/debian buster/main arm64 mscgen arm64 0.20-12 [48.8 kB] Get: 230 http://deb.debian.org/debian buster/main arm64 preview-latex-style all 11.91-2 [201 kB] Get: 231 http://deb.debian.org/debian buster/main arm64 python-alabaster all 0.7.8-1 [18.4 kB] Get: 232 http://deb.debian.org/debian buster/main arm64 python-babel-localedata all 2.6.0+dfsg.1-1 [4083 kB] Get: 233 http://deb.debian.org/debian buster/main arm64 python-pkg-resources all 40.8.0-1 [182 kB] Get: 234 http://deb.debian.org/debian buster/main arm64 python-tz all 2019.1-1 [33.6 kB] Get: 235 http://deb.debian.org/debian buster/main arm64 python-babel all 2.6.0+dfsg.1-1 [97.3 kB] Get: 236 http://deb.debian.org/debian buster/main arm64 python-certifi all 2018.8.24-1 [140 kB] Get: 237 http://deb.debian.org/debian buster/main arm64 python-chardet all 3.0.4-3 [80.6 kB] Get: 238 http://deb.debian.org/debian buster/main arm64 python-roman all 2.0.0-3 [8688 B] Get: 239 http://deb.debian.org/debian buster/main arm64 python-docutils all 0.14+dfsg-4 [379 kB] Get: 240 http://deb.debian.org/debian buster/main arm64 python-idna all 2.6-1 [34.1 kB] Get: 241 http://deb.debian.org/debian buster/main arm64 python-imagesize all 1.0.0-1 [4888 B] Get: 242 http://deb.debian.org/debian buster/main arm64 python-markupsafe arm64 1.1.0-1 [14.0 kB] Get: 243 http://deb.debian.org/debian buster/main arm64 python-jinja2 all 2.10-2 [106 kB] Get: 244 http://deb.debian.org/debian buster/main arm64 python-pyparsing all 2.2.0+dfsg1-2 [89.5 kB] Get: 245 http://deb.debian.org/debian buster/main arm64 python-six all 1.12.0-1 [15.7 kB] Get: 246 http://deb.debian.org/debian buster/main arm64 python-packaging all 19.0-1 [20.4 kB] Get: 247 http://deb.debian.org/debian buster/main arm64 python-pygments all 2.3.1+dfsg-1 [596 kB] Get: 248 http://deb.debian.org/debian buster/main arm64 python-urllib3 all 1.24.1-1 [97.0 kB] Get: 249 http://deb.debian.org/debian buster/main arm64 python-requests all 2.21.0-1 [67.1 kB] Get: 250 http://deb.debian.org/debian buster/main arm64 python-typing all 3.6.6-1 [22.7 kB] Get: 251 http://deb.debian.org/debian buster/main arm64 sphinx-common all 1.8.4-1 [500 kB] Get: 252 http://deb.debian.org/debian buster/main arm64 python-sphinx all 1.8.4-1 [482 kB] Get: 253 http://deb.debian.org/debian buster/main arm64 rdfind arm64 1.4.1-1 [38.3 kB] Get: 254 http://deb.debian.org/debian buster/main arm64 symlinks arm64 1.4-3+b1 [10.6 kB] Get: 255 http://deb.debian.org/debian buster/main arm64 t1utils arm64 1.41-3 [59.7 kB] Get: 256 http://deb.debian.org/debian buster/main arm64 texlive-binaries arm64 2018.20181218.49446-1 [8464 kB] Get: 257 http://deb.debian.org/debian buster/main arm64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get: 258 http://deb.debian.org/debian buster/main arm64 texlive-base all 2018.20190227-2 [19.7 MB] Get: 259 http://deb.debian.org/debian buster/main arm64 texlive-fonts-recommended all 2018.20190227-2 [5228 kB] Get: 260 http://deb.debian.org/debian buster/main arm64 texlive-latex-base all 2018.20190227-2 [984 kB] Get: 261 http://deb.debian.org/debian buster/main arm64 texlive-latex-recommended all 2018.20190227-2 [15.2 MB] Get: 262 http://deb.debian.org/debian buster/main arm64 texlive-pictures all 2018.20190227-2 [8201 kB] Get: 263 http://deb.debian.org/debian buster/main arm64 texlive-latex-extra all 2018.20190227-2 [12.3 MB] Get: 264 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 200 MB in 13s (15.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u4_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u4) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../14-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:arm64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:arm64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython2-stdlib:arm64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:arm64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (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 ... 20664 files and directories currently installed.) Preparing to unpack .../000-python_2.7.16-1_arm64.deb ... Unpacking python (2.7.16-1) ... Selecting previously unselected package libfftw3-double3:arm64. Preparing to unpack .../001-libfftw3-double3_3.3.8-2_arm64.deb ... Unpacking libfftw3-double3:arm64 (3.3.8-2) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../002-libpng16-16_1.6.36-6_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.36-6) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../003-libfreetype6_2.9.1-3+deb10u2_arm64.deb ... Unpacking libfreetype6:arm64 (2.9.1-3+deb10u2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package ucf. Preparing to unpack .../005-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../006-fonts-dejavu-core_2.37-1_all.deb ... Unpacking fonts-dejavu-core (2.37-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../007-fontconfig-config_2.13.1-2_all.deb ... Unpacking fontconfig-config (2.13.1-2) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../008-libfontconfig1_2.13.1-2_arm64.deb ... Unpacking libfontconfig1:arm64 (2.13.1-2) ... Selecting previously unselected package libde265-0:arm64. Preparing to unpack .../009-libde265-0_1.0.3-1+b1_arm64.deb ... Unpacking libde265-0:arm64 (1.0.3-1+b1) ... Selecting previously unselected package libnuma1:arm64. Preparing to unpack .../010-libnuma1_2.0.12-1_arm64.deb ... Unpacking libnuma1:arm64 (2.0.12-1) ... Selecting previously unselected package libx265-165:arm64. Preparing to unpack .../011-libx265-165_2.9-4_arm64.deb ... Unpacking libx265-165:arm64 (2.9-4) ... Selecting previously unselected package libheif1:arm64. Preparing to unpack .../012-libheif1_1.3.2-2~deb10u1_arm64.deb ... Unpacking libheif1:arm64 (1.3.2-2~deb10u1) ... Selecting previously unselected package libjbig0:arm64. Preparing to unpack .../013-libjbig0_2.1-3.1+b2_arm64.deb ... Unpacking libjbig0:arm64 (2.1-3.1+b2) ... Selecting previously unselected package libjpeg62-turbo:arm64. Preparing to unpack .../014-libjpeg62-turbo_1%3a1.5.2-2+deb10u1_arm64.deb ... Unpacking libjpeg62-turbo:arm64 (1:1.5.2-2+deb10u1) ... Selecting previously unselected package liblcms2-2:arm64. Preparing to unpack .../015-liblcms2-2_2.9-3_arm64.deb ... Unpacking liblcms2-2:arm64 (2.9-3) ... Selecting previously unselected package libglib2.0-0:arm64. Preparing to unpack .../016-libglib2.0-0_2.58.3-2+deb10u2_arm64.deb ... Unpacking libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... Selecting previously unselected package liblqr-1-0:arm64. Preparing to unpack .../017-liblqr-1-0_0.4.2-2.1_arm64.deb ... Unpacking liblqr-1-0:arm64 (0.4.2-2.1) ... Selecting previously unselected package libltdl7:arm64. Preparing to unpack .../018-libltdl7_2.4.6-9_arm64.deb ... Unpacking libltdl7:arm64 (2.4.6-9) ... Selecting previously unselected package libopenjp2-7:arm64. Preparing to unpack .../019-libopenjp2-7_2.3.0-2+deb10u1_arm64.deb ... Unpacking libopenjp2-7:arm64 (2.3.0-2+deb10u1) ... Selecting previously unselected package libwebp6:arm64. Preparing to unpack .../020-libwebp6_0.6.1-2_arm64.deb ... Unpacking libwebp6:arm64 (0.6.1-2) ... Selecting previously unselected package libtiff5:arm64. Preparing to unpack .../021-libtiff5_4.1.0+git191117-2~deb10u1_arm64.deb ... Unpacking libtiff5:arm64 (4.1.0+git191117-2~deb10u1) ... Selecting previously unselected package libwebpmux3:arm64. Preparing to unpack .../022-libwebpmux3_0.6.1-2_arm64.deb ... Unpacking libwebpmux3:arm64 (0.6.1-2) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../023-libxau6_1%3a1.0.8-1+b2_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.8-1+b2) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../024-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../025-libxcb1_1.13.1-2_arm64.deb ... Unpacking libxcb1:arm64 (1.13.1-2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../026-libx11-data_2%3a1.6.7-1+deb10u1_all.deb ... Unpacking libx11-data (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../027-libx11-6_2%3a1.6.7-1+deb10u1_arm64.deb ... Unpacking libx11-6:arm64 (2:1.6.7-1+deb10u1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../028-libxext6_2%3a1.3.3-1+b2_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.3-1+b2) ... Selecting previously unselected package libicu63:arm64. Preparing to unpack .../029-libicu63_63.1-6+deb10u1_arm64.deb ... Unpacking libicu63:arm64 (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../030-libxml2_2.9.4+dfsg1-7+deb10u1_arm64.deb ... Unpacking libxml2:arm64 (2.9.4+dfsg1-7+deb10u1) ... Selecting previously unselected package imagemagick-6-common. Preparing to unpack .../031-imagemagick-6-common_8%3a6.9.10.23+dfsg-2.1+deb10u1_all.deb ... Unpacking imagemagick-6-common (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickcore-6.q16-6:arm64. Preparing to unpack .../032-libmagickcore-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_arm64.deb ... Unpacking libmagickcore-6.q16-6:arm64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package libmagickwand-6.q16-6:arm64. Preparing to unpack .../033-libmagickwand-6.q16-6_8%3a6.9.10.23+dfsg-2.1+deb10u1_arm64.deb ... Unpacking libmagickwand-6.q16-6:arm64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../034-poppler-data_0.4.9-2_all.deb ... Unpacking poppler-data (0.4.9-2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../035-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package tex-common. Preparing to unpack .../036-tex-common_6.11_all.deb ... Unpacking tex-common (6.11) ... Selecting previously unselected package libncurses6:arm64. Preparing to unpack .../037-libncurses6_6.1+20181013-2+deb10u2_arm64.deb ... Unpacking libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Selecting previously unselected package libprocps7:arm64. Preparing to unpack .../038-libprocps7_2%3a3.3.15-2_arm64.deb ... Unpacking libprocps7:arm64 (2:3.3.15-2) ... Selecting previously unselected package lsb-base. Preparing to unpack .../039-lsb-base_10.2019051400_all.deb ... Unpacking lsb-base (10.2019051400) ... Selecting previously unselected package procps. Preparing to unpack .../040-procps_2%3a3.3.15-2_arm64.deb ... Unpacking procps (2:3.3.15-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../041-libmagic-mgc_1%3a5.35-4+deb10u2_arm64.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u2) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../042-libmagic1_1%3a5.35-4+deb10u2_arm64.deb ... Unpacking libmagic1:arm64 (1:5.35-4+deb10u2) ... Selecting previously unselected package file. Preparing to unpack .../043-file_1%3a5.35-4+deb10u2_arm64.deb ... Unpacking file (1:5.35-4+deb10u2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../044-gettext-base_0.19.8.1-9_arm64.deb ... Unpacking gettext-base (0.19.8.1-9) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../045-libedit2_3.1-20181209-1_arm64.deb ... Unpacking libedit2:arm64 (3.1-20181209-1) ... Selecting previously unselected package libkeyutils1:arm64. Preparing to unpack .../046-libkeyutils1_1.6-6_arm64.deb ... Unpacking libkeyutils1:arm64 (1.6-6) ... Selecting previously unselected package libkrb5support0:arm64. Preparing to unpack .../047-libkrb5support0_1.17-3+deb10u1_arm64.deb ... Unpacking libkrb5support0:arm64 (1.17-3+deb10u1) ... Selecting previously unselected package libk5crypto3:arm64. Preparing to unpack .../048-libk5crypto3_1.17-3+deb10u1_arm64.deb ... Unpacking libk5crypto3:arm64 (1.17-3+deb10u1) ... Selecting previously unselected package libkrb5-3:arm64. Preparing to unpack .../049-libkrb5-3_1.17-3+deb10u1_arm64.deb ... Unpacking libkrb5-3:arm64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:arm64. Preparing to unpack .../050-libgssapi-krb5-2_1.17-3+deb10u1_arm64.deb ... Unpacking libgssapi-krb5-2:arm64 (1.17-3+deb10u1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../051-openssh-client_1%3a7.9p1-10+deb10u2_arm64.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../052-libsigsegv2_2.12-2_arm64.deb ... Unpacking libsigsegv2:arm64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../053-m4_1.4.18-2_arm64.deb ... 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Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libnl-3-200:arm64 (3.4.0-1) ... Setting up openmpi-common (3.1.3-11) ... Setting up fonts-lmodern (2.004.5-6) ... Setting up libopenjp2-7:arm64 (2.3.0-2+deb10u1) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:arm64 (1.8.0-2.1) ... Setting up xorg-sgml-doctools (1:1.11-1) ... Setting up sgml-base (1.29) ... Setting up cmake-data (3.13.4-1) ... Setting up libcdt5 (2.40.1-6) ... Setting up libkrb5-3:arm64 (1.17-3+deb10u1) ... Setting up libcgraph6 (2.40.1-6) ... Setting up libboost-dev:arm64 (1.67.0.1) ... Setting up libtiff5:arm64 (4.1.0+git191117-2~deb10u1) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up libde265-0:arm64 (1.0.3-1+b1) ... Setting up openssl (1.1.1d-0+deb10u4) ... Setting up libwebpmux3:arm64 (0.6.1-2) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... 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Setting up libx265-165:arm64 (2.9-4) ... Setting up libhwloc5:arm64 (1.11.12-3) ... Setting up gfortran-8 (8.3.0-6) ... Setting up libedit2:arm64 (3.1-20181209-1) ... Setting up libheif1:arm64 (1.3.2-2~deb10u1) ... Setting up hwloc-nox (1.11.12-3) ... Setting up libavahi-common3:arm64 (0.7-4+b1) ... Setting up libldap-2.4-2:arm64 (2.4.47+dfsg-3+deb10u4) ... Setting up m4 (1.4.18-2) ... Setting up libxcb-shm0:arm64 (1.13.1-2) ... Setting up libhwloc-plugins:arm64 (1.11.12-3) ... Setting up libllvm6.0:arm64 (1:6.0.1-10) ... Setting up gfortran (4:8.3.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libclang1-6.0:arm64 (1:6.0.1-10) ... Setting up libnuma-dev:arm64 (2.0.12-1) ... Setting up libnl-route-3-200:arm64 (3.4.0-1) ... Setting up libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Setting up libthai0:arm64 (0.1.28-2) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up libblas3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up doxygen (1.8.13-10) ... Setting up libptexenc1:arm64 (2018.20181218.49446-1) ... Setting up libfreetype6:arm64 (2.9.1-3+deb10u2) ... Setting up x11proto-core-dev (2018.4-4) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:arm64 (1.17-3+deb10u1) ... Setting up libcroco3:arm64 (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up autoconf (2.69-11) ... Setting up libgvpr2 (2.40.1-6) ... Setting up dwz (0.12-3) ... Setting up libnl-3-dev:arm64 (3.4.0-1) ... Setting up groff-base (1.22.4-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libcurl4:arm64 (7.64.0-4+deb10u1) ... Setting up libx11-6:arm64 (2:1.6.7-1+deb10u1) ... Setting up libharfbuzz0b:arm64 (2.3.1-1) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libfftw3-dev:arm64 (3.3.8-2) ... Setting up libavahi-client3:arm64 (0.7-4+b1) ... Setting up libblas-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:arm64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libibverbs1:arm64 (22.1-1) ... Setting up liblapack3:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libharfbuzz-icu0:arm64 (2.3.1-1) ... Setting up libxcb1-dev:arm64 (1.13.1-2) ... Setting up libxpm4:arm64 (1:3.5.12-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libpmix2:arm64 (3.1.2-3) ... Setting up ibverbs-providers:arm64 (22.1-1) ... Setting up libpython2-stdlib:arm64 (2.7.16-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up mpich (3.3-3) ... update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up libopenmpi3:arm64 (3.1.3-11) ... Setting up libx11-dev:arm64 (2:1.6.7-1+deb10u1) ... Setting up libxext6:arm64 (2:1.3.3-1+b2) ... Setting up libpaper-utils (1.1.28) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up tex-common (6.11) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:arm64 (3.4.0-1) ... Setting up libltdl-dev:arm64 (2.4.6-9) ... Setting up libpython-stdlib:arm64 (2.7.16-1) ... Setting up sphinx-common (1.8.4-1) ... Setting up liblapack-dev:arm64 (3.8.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode Setting up libmpich-dev:arm64 (3.3-3) ... update-alternatives: using /usr/include/aarch64-linux-gnu/mpich to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-linux-gnu) in auto mode Setting up libxt6:arm64 (1:1.1.5-1+b3) ... Setting up libcups2:arm64 (2.2.10-6+deb10u4) ... Setting up cmake (3.13.4-1) ... Setting up libhwloc-dev:arm64 (1.11.12-3) ... Setting up libfontconfig1:arm64 (2.13.1-2) ... Setting up python (2.7.16-1) ... Setting up openmpi-bin (3.1.3-11) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxmu6:arm64 (2:1.1.2-2+b3) ... Setting up libxi6:arm64 (2:1.7.9-1) ... Setting up python-typing (3.6.6-1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up preview-latex-style (11.91-2) ... Setting up libpango-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up libxaw7:arm64 (2:1.0.13-1+b2) ... Setting up libibverbs-dev:arm64 (22.1-1) ... Setting up python-certifi (2018.8.24-1) ... Setting up python-pygments (2.3.1+dfsg-1) ... Setting up libcairo2:arm64 (1.16.0-4+deb10u1) ... Setting up libcupsimage2:arm64 (2.2.10-6+deb10u4) ... Setting up python-six (1.12.0-1) ... Setting up python-pyparsing (2.2.0+dfsg1-2) ... Setting up libmagickcore-6.q16-6:arm64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up python-imagesize (1.0.0-1) ... Setting up python-idna (2.6-1) ... Setting up libgd3:arm64 (2.2.5-5.2) ... Setting up python-markupsafe (1.1.0-1) ... Setting up python-roman (2.0.0-3) ... Setting up python-tz (2019.1-1) ... Setting up python-alabaster (0.7.8-1) ... Setting up libmagickwand-6.q16-6:arm64 (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up python-chardet (3.0.4-3) ... Setting up python-babel (2.6.0+dfsg.1-1) ... update-alternatives: using /usr/bin/pybabel-python2 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libopenmpi-dev:arm64 (3.1.3-11) ... 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 (1.42.4-8~deb10u1) ... Setting up libpangocairo-1.0-0:arm64 (1.42.4-8~deb10u1) ... Setting up python-packaging (19.0-1) ... Setting up python-urllib3 (1.24.1-1) ... Setting up libgs9:arm64 (9.27~dfsg-2+deb10u4) ... Setting up mscgen (0.20-12) ... Setting up ghostscript (9.27~dfsg-2+deb10u4) ... Setting up python-jinja2 (2.10-2) ... Setting up libgvc6 (2.40.1-6) ... Setting up imagemagick-6.q16 (8:6.9.10.23+dfsg-2.1+deb10u1) ... update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare (compare) in auto mode update-alternatives: using /usr/bin/compare-im6.q16 to provide /usr/bin/compare-im6 (compare-im6) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate (animate) in auto mode update-alternatives: using /usr/bin/animate-im6.q16 to provide /usr/bin/animate-im6 (animate-im6) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert (convert) in auto mode update-alternatives: using /usr/bin/convert-im6.q16 to provide /usr/bin/convert-im6 (convert-im6) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite (composite) in auto mode update-alternatives: using /usr/bin/composite-im6.q16 to provide /usr/bin/composite-im6 (composite-im6) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure (conjure) in auto mode update-alternatives: using /usr/bin/conjure-im6.q16 to provide /usr/bin/conjure-im6 (conjure-im6) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import (import) in auto mode update-alternatives: using /usr/bin/import-im6.q16 to provide /usr/bin/import-im6 (import-im6) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify (identify) in auto mode update-alternatives: using /usr/bin/identify-im6.q16 to provide /usr/bin/identify-im6 (identify-im6) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream (stream) in auto mode update-alternatives: using /usr/bin/stream-im6.q16 to provide /usr/bin/stream-im6 (stream-im6) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display (display) in auto mode update-alternatives: using /usr/bin/display-im6.q16 to provide /usr/bin/display-im6 (display-im6) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage (montage) in auto mode update-alternatives: using /usr/bin/montage-im6.q16 to provide /usr/bin/montage-im6 (montage-im6) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify (mogrify) in auto mode update-alternatives: using /usr/bin/mogrify-im6.q16 to provide /usr/bin/mogrify-im6 (mogrify-im6) in auto mode Setting up texlive-binaries (2018.20181218.49446-1) ... 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 python-requests (2.21.0-1) ... Setting up texlive-base (2018.20190227-2) ... 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/config/pdftexconfig.tex Setting up graphviz (2.40.1-6) ... Setting up texlive-latex-base (2018.20190227-2) ... Setting up texlive-latex-recommended (2018.20190227-2) ... Setting up texlive-pictures (2018.20190227-2) ... Setting up imagemagick (8:6.9.10.23+dfsg-2.1+deb10u1) ... Setting up texlive-fonts-recommended (2018.20190227-2) ... Setting up texlive-latex-extra (2018.20190227-2) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for sgml-base (1.29) ... Setting up docutils-common (0.14+dfsg-4) ... Processing triggers for sgml-base (1.29) ... Setting up python-docutils (0.14+dfsg-4) ... update-alternatives: using /usr/share/docutils/scripts/python2/rst-buildhtml to provide /usr/bin/rst-buildhtml (rst-buildhtml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html to provide /usr/bin/rst2html (rst2html) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html4 to provide /usr/bin/rst2html4 (rst2html4) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2html5 to provide /usr/bin/rst2html5 (rst2html5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2latex to provide /usr/bin/rst2latex (rst2latex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2man to provide /usr/bin/rst2man (rst2man) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt to provide /usr/bin/rst2odt (rst2odt) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2odt_prepstyles to provide /usr/bin/rst2odt_prepstyles (rst2odt_prepstyles) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2pseudoxml to provide /usr/bin/rst2pseudoxml (rst2pseudoxml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2s5 to provide /usr/bin/rst2s5 (rst2s5) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xetex to provide /usr/bin/rst2xetex (rst2xetex) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rst2xml to provide /usr/bin/rst2xml (rst2xml) in auto mode update-alternatives: using /usr/share/docutils/scripts/python2/rstpep2html to provide /usr/bin/rstpep2html (rstpep2html) in auto mode Setting up python-sphinx (1.8.4-1) ... update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-apidoc to provide /usr/bin/sphinx-apidoc (sphinx-apidoc) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-autogen to provide /usr/bin/sphinx-autogen (sphinx-autogen) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-build to provide /usr/bin/sphinx-build (sphinx-build) in auto mode update-alternatives: using /usr/share/sphinx/scripts/python2/sphinx-quickstart to provide /usr/bin/sphinx-quickstart (sphinx-quickstart) in auto mode Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.11) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/gromacs-2019.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../gromacs_2019.1-1_source.changes dpkg-buildpackage: info: source package gromacs dpkg-buildpackage: info: source version 2019.1-1 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 rm -rf build docs/doxygen/*.pyc dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \ debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian debian/rules binary dh_testdir (mkdir -p build/basic; cd build/basic; cmake /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- 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 -- Found X11: /usr/lib/aarch64-linux-gnu/libX11.so -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3f, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" -- Could not convert sample image, ImageMagick convert can not be used -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/basic (mkdir -p build/basic-dp; cd build/basic-dp; cmake /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- 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 -- Found X11: /usr/lib/aarch64-linux-gnu/libX11.so -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "_d" -- Using default library suffix: "_d" -- Could not convert sample image, ImageMagick convert can not be used -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/basic-dp (mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.mpich -- Check for working C compiler: /usr/bin/mpicc.mpich -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3f, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.mpich" -- Using manually set library suffix: "_mpi.mpich" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/mpich (mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.mpich -- Check for working C compiler: /usr/bin/mpicc.mpich -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- Check for working CXX compiler: /usr/bin/mpicxx.mpich -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.mpich" -- Using manually set library suffix: "_mpi_d.mpich" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/mpich-dp (mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.openmpi -- Check for working C compiler: /usr/bin/mpicc.openmpi -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Looking for NVIDIA GPUs present in the system -- Could not detect NVIDIA GPUs -- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3f, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi.openmpi" -- Using manually set library suffix: "_mpi.openmpi" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/openmpi (mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \ /build/gromacs-2019.1 -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DGMX_EXTERNAL_ZLIB=ON -DGMX_SIMD=ARM_NEON_ASIMD -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi") -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/mpicc.openmpi -- Check for working C compiler: /usr/bin/mpicc.openmpi -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- Check for working CXX compiler: /usr/bin/mpicxx.openmpi -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success CMake Warning at cmake/gmxManageGPU.cmake:53 (message): GPU acceleration is not available in double precision, disabled! Call Stack (most recent call first): CMakeLists.txt:229 (include) -- 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_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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- MPI is not compatible with thread-MPI. Disabling thread-MPI. -- Checking for MPI_IN_PLACE -- Performing Test MPI_IN_PLACE_COMPILE_OK -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success -- Checking for MPI_IN_PLACE - yes -- Defaulting to building static libraries -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - Success -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.11") -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so -- Looking for zlibVersion in /usr/lib/aarch64-linux-gnu/libz.so - found -- 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.) -- Not using dynamic plugins (e.g VMD-supported file formats) -- Using manually set binary suffix: "_mpi_d.openmpi" -- Using manually set library suffix: "_mpi_d.openmpi" -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/openmpi-dp touch configure-stamp dh_testdir /usr/bin/make -j8 -C build/basic make[1]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles /build/gromacs-2019.1/build/basic/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target view_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build Scanning dependencies of target tng_io_obj make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-2019.1/src/programs/view/3dview.cpp make[3]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /build/gromacs-2019.1/src/programs/view/buttons.cpp Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' Scanning dependencies of target mdrun_test_objlib /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energyreader.cpp Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/gromacs-2019.1/src/programs/view/dialogs.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/gromacs-2019.1/src/programs/view/fgrid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-2019.1/src/programs/view/filter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /build/gromacs-2019.1/src/programs/view/logo.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 1%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /build/gromacs-2019.1/src/programs/view/manager.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /build/gromacs-2019.1/src/programs/view/molps.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energycomparison.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src 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-DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /build/gromacs-2019.1/src/programs/view/xdlghi.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/src/programs/mdrun/tests/moduletest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /build/gromacs-2019.1/src/programs/view/xdlgitem.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/simulationdatabase.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /build/gromacs-2019.1/src/programs/view/xmb.cpp cd /build/gromacs-2019.1/build/basic/src/programs && /usr/bin/c++ 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/terminationhelper.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 2%] Built target view_objlib cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/event.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/group.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/group.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/topology.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/list.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/type.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 2%] Built target mdrun_test_objlib cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 4%] Built target tng_io_obj cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 8%] Built target libgromacs_external cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 24%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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-isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicCommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicCommunicator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mimic/MimicUtils.cpp.o -c /build/gromacs-2019.1/src/gromacs/mimic/MimicUtils.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /build/gromacs-2019.1/build/basic/src/gromacs/utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,:::::::::::::::::::::::::::::::: /usr/lib/aarch64-linux-gnu/libhwloc.so -ldl -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lpthread -fopenmp -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblapack.so -lpthread -lm cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/share/template /build/gromacs-2019.1/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic 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target mdrun_objlib Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp Scanning dependencies of target mdrun_test_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/energyreader.cpp Scanning dependencies of target view_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /build/gromacs-2019.1/src/programs/view/3dview.cpp Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /build/gromacs-2019.1/src/programs/view/buttons.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /build/gromacs-2019.1/src/programs/view/dialogs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 1%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /build/gromacs-2019.1/src/programs/view/fgrid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 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/build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /build/gromacs-2019.1/src/programs/view/filter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/basic-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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/build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /build/gromacs-2019.1/src/programs/view/nmol.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/moduletest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /build/gromacs-2019.1/src/programs/view/xutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/alltoall.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/p2p_protocol.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 2%] Built target view_objlib cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/barrier.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/barrier.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/collective.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/collective.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused 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/build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/profile.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/profile.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/comm.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/comm.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/terminationhelper.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/event.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/event.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/reduce_fast.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/gather.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/gather.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scatter.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scatter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/group.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/group.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_init.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/topology.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/topology.cpp [ 4%] Built target tng_io_obj cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectorycomparison.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/list.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/list.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/type.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 8%] Built target libgromacs_external cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectoryreader.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 8%] Built target mdrun_test_objlib cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 24%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 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/build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit 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cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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/build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/timeunitmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs_d.so.4 -o ../../lib/libgromacs_d.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,:::::::::::::::::::::::::::::::: /usr/lib/aarch64-linux-gnu/libhwloc.so -ldl -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 -lpthread -fopenmp -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblapack.so -lpthread -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.4.0.0 ../../lib/libgromacs_d.so.4 ../../lib/libgromacs_d.so make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/share/template /build/gromacs-2019.1/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= Scanning dependencies of target template make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/share/template && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/template.dir/template.cpp.o -c /build/gromacs-2019.1/share/template/template.cpp Scanning dependencies of target gmx make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/gmx.dir/gmx.cpp.o -c /build/gromacs-2019.1/src/programs/gmx.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs && 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make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target gmx cd /build/gromacs-2019.1/build/basic-dp/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/template.dir/template.cpp.o -o ../../bin/template -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../lib/libgromacs_d.so.4.0.0 -fopenmp -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target template make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -j8 -C build/basic tests 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/build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/external/googletest /build/gromacs-2019.1/build/basic/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs 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/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 3%] Built target libgromacs_external Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 4%] Built target tng_io_obj /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/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 4%] Built target lmfit_objlib /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/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/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc [ 4%] Built target mdrun_test_objlib /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc [ 5%] Built target mdrun_objlib [ 19%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.cpp Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/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 cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/vsite.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/applied-forces/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/listed-forces.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/listed-forces.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/manage-threading.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/manage-threading.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/orires.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/orires.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/pairs.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/pairs.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target onlinehelp-test-shared cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/position-restraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/position-restraints.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/listed-forces/restcbt.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/restcbt.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/ewald-utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/ewald-utils.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/basic/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -shared -Wl,-soname,libgromacs.so.4 -o ../../lib/libgromacs.so.4.0.0 @CMakeFiles/libgromacs.dir/objects1.rsp -Wl,-rpath,:::::::::::::::::::::::::::::::: /usr/lib/aarch64-linux-gnu/libhwloc.so -ldl -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so -lpthread -fopenmp -lm /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblapack.so -lpthread -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 19%] Built target analysisdata-test-shared cd /build/gromacs-2019.1/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.4.0.0 ../../lib/libgromacs.so.4 ../../lib/libgromacs.so make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 79%] Built target libgromacs cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 79%] 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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/testutils /build/gromacs-2019.1/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem 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/build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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-fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o 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/build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/domain_decomposition.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target listed-forces-test Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/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]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp Scanning dependencies of target applied-forces-test make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Leaving directory '/build/gromacs-2019.1/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 Scanning dependencies of target commandline-test make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] Built target testutils-mpi-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] Built target listed-forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] Built target applied-forces-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 80%] 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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 82%] Built target fft-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/math/tests /build/gromacs-2019.1/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-2019.1/build/basic/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 82%] Built target hardware-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../lib/libtestutils.a ../../../lib/libgromacs.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target testutils-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target mdrunutility-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target mdrunutility-mpi-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/options/tests /build/gromacs-2019.1/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 83%] Built target mdrun-mpi-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/random/tests /build/gromacs-2019.1/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 84%] Built target gpu_utils-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target mdlib-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target restraintpotential-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /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]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 85%] Built target taskassignment-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target commandline-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target ewald-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target pull-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target table-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target fileio-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 86%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 88%] Built target math-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_trjconv.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 89%] Built target awh-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/solvate.cpp /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_msd.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 89%] Built target pdb2gmx-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/expfit.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 89%] Built target gmxpreprocess-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/indexutil.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 90%] Built target gmxana-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] 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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target correlations-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/tests/report-methods.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target energyanalysis-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target tool-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target legacy-mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tpitest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 91%] Built target legacy-mdrun-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/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/average.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectioncollection.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 92%] Built target options-test cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 94%] Built target mdrun-non-integrator-test cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 94%] Built target analysisdata-test cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.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 ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 96%] Built target trajectoryanalysis-test cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/toputils.cpp cd /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 96%] Built target mdrun-test cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target simd-test cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target selection-test cd /build/gromacs-2019.1/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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 -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' make[1]: Leaving directory '/build/gromacs-2019.1/build/basic' (cd build/basic; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic/DartConfiguration.tcl Test project /build/gromacs-2019.1/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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/basic/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (4 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (10 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (9 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (19 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (2 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (31 ms total) 1: [ PASSED ] 59 tests. 1/40 Test #1: TestUtilsUnitTests ............... Passed 0.05 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-2019.1/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (10 ms) 2: [----------] 1 test from MpiSelfTest (10 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (10 ms total) 2: [ PASSED ] 1 test. 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.04 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/basic/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (1 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (1 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (1 ms) 3: [----------] 1 test from NullSignalTest (1 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (0 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (4 ms total) 3: [ PASSED ] 50 tests. 3/40 Test #3: MdlibUnitTest .................... Passed 0.03 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/basic/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (0 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (1 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 3 tests. 4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.02 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/basic/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (1 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (1 ms) 5: [----------] 15 tests from BondedTest (2 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (2 ms total) 5: [ PASSED ] 15 tests. 5/40 Test #5: ListedForcesTest ................. Passed 0.03 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/basic/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (10 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (11 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (20 ms total) 6: [ PASSED ] 55 tests. 6/40 Test #6: CommandLineUnitTests ............. Passed 0.06 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/basic/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (0 ms total) 7: [ PASSED ] 9 tests. 7/40 Test #7: DomDecTests ...................... Passed 0.02 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/basic/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (45 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (68 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (23 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (0 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (8 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (13 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (21 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (24 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (27 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (82 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (379 ms total) 8: [ PASSED ] 257 tests. 8/40 Test #8: EwaldUnitTests ................... Passed 0.44 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/basic/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (8 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (16 ms) 9: [----------] 2 tests from ManyFFTTest (25 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 9: [----------] 1 test from FFTTest (5 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 9: [----------] 1 test from FFFTest3D (3 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (5 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (8 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (10 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (36 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (70 ms total) 9: [ PASSED ] 14 tests. 9/40 Test #9: FFTUnitTests ..................... Passed 0.09 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/basic/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (2 ms total) 10: [ PASSED ] 60 tests. 10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.03 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/basic/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (22 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (22 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (20 ms) 11: [----------] 4 tests from HardwareTopologyTest (84 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (84 ms total) 11: [ PASSED ] 4 tests. 11/40 Test #11: HardwareUnitTests ................ Passed 0.10 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/basic/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (0 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (0 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (1 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (0 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (3 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (1 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (6 ms total) 12: [ PASSED ] 112 tests. 12/40 Test #12: MathUnitTests .................... Passed 0.03 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/basic/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (5 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 13: [----------] 17 tests from ThreadAffinityTest (9 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (9 ms total) 13: [ PASSED ] 17 tests. 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.03 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /build/gromacs-2019.1/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (69 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (52 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (43 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (40 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (96 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (40 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (342 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (47 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (40 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (55 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (56 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (35 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (56 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (39 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (331 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (673 ms total) 14: [ PASSED ] 13 tests. 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.69 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/basic/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (1 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (1 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (4 ms total) 15: [ PASSED ] 22 tests. 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.02 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/basic/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (1 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (1 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (1 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (1 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (3 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (10 ms total) 16: [ PASSED ] 110 tests. 16/40 Test #16: OptionsUnitTests ................. Passed 0.04 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/basic/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (0 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (0 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (1 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (7 ms total) 17: [ PASSED ] 44 tests. 17/40 Test #17: RandomUnitTests .................. Passed 0.04 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/basic/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (1 ms) 18: [----------] 1 test from RestraintManager (1 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (1 ms total) 18: [ PASSED ] 1 test. 18/40 Test #18: RestraintTests ................... Passed 0.02 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/basic/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (1 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (33 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (65 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (70 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (17 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (64 ms) 19: [----------] 10 tests from SplineTableTest/0 (261 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (1 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (6 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (3 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (10 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (12 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (4 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (10 ms) 19: [----------] 10 tests from SplineTableTest/1 (52 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (313 ms total) 19: [ PASSED ] 20 tests. 19/40 Test #19: TableUnitTests ................... Passed 0.33 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/basic/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.02 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/basic/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (1 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (3 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (0 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (1 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (1 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (2 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (2 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (1 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (2 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (20 ms total) 21: [ PASSED ] 325 tests. 21/40 Test #21: UtilityUnitTests ................. Passed 0.05 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /build/gromacs-2019.1/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (20 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (24 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (44 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (44 ms total) 22: [ PASSED ] 2 tests. 22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.07 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/basic/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms) 23: [----------] 2 tests from FileMD5Test (2 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (7 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (10 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (12 ms total) 23: [ PASSED ] 17 tests. 23/40 Test #23: FileIOTests ...................... Passed 0.03 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/basic/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (1 ms total) 24: [ PASSED ] 5 tests. 24/40 Test #24: PullTest ......................... Passed 0.02 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/basic/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (2 ms) 25: [----------] 1 test from gridTest (2 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (9 ms total) 25: [ PASSED ] 12 tests. 25/40 Test #25: AwhTest .......................... Passed 0.03 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/basic/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 277 tests from 22 test cases. 26: [----------] Global test environment set-up. 26: [----------] 9 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadStore 26: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadU 26: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4StoreU 26: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 26: [----------] 9 tests from SimdBootstrapTest (1 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (1 ms total) 26: 26: [----------] 16 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 26: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 26: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 26: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 26: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (0 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (1 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (1 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (2 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (0 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (1 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (2 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (0 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (2 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (2 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (2 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (1 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (2 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (9 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (1 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (1 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (9 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (2 ms) 26: [----------] 45 tests from SimdMathTest (64 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (0 ms total) 26: 26: [----------] 32 tests from Simd4FloatingpointTest 26: [ RUN ] Simd4FloatingpointTest.setZero 26: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 26: [ RUN ] Simd4FloatingpointTest.set 26: [ OK ] Simd4FloatingpointTest.set (0 ms) 26: [ RUN ] Simd4FloatingpointTest.add 26: [ OK ] Simd4FloatingpointTest.add (0 ms) 26: [ RUN ] Simd4FloatingpointTest.sub 26: [ OK ] Simd4FloatingpointTest.sub (0 ms) 26: [ RUN ] Simd4FloatingpointTest.mul 26: [ OK ] Simd4FloatingpointTest.mul (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fma 26: [ OK ] Simd4FloatingpointTest.fma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fms 26: [ OK ] Simd4FloatingpointTest.fms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnma 26: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnms 26: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.abs 26: [ OK ] Simd4FloatingpointTest.abs (0 ms) 26: [ RUN ] Simd4FloatingpointTest.neg 26: [ OK ] Simd4FloatingpointTest.neg (0 ms) 26: [ RUN ] Simd4FloatingpointTest.and 26: [ OK ] Simd4FloatingpointTest.and (0 ms) 26: [ RUN ] Simd4FloatingpointTest.or 26: [ OK ] Simd4FloatingpointTest.or (0 ms) 26: [ RUN ] Simd4FloatingpointTest.xor 26: [ OK ] Simd4FloatingpointTest.xor (1 ms) 26: [ RUN ] Simd4FloatingpointTest.andNot 26: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 26: [ RUN ] Simd4FloatingpointTest.max 26: [ OK ] Simd4FloatingpointTest.max (0 ms) 26: [ RUN ] Simd4FloatingpointTest.min 26: [ OK ] Simd4FloatingpointTest.min (0 ms) 26: [ RUN ] Simd4FloatingpointTest.round 26: [ OK ] Simd4FloatingpointTest.round (0 ms) 26: [ RUN ] Simd4FloatingpointTest.trunc 26: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 26: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 26: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.selectByNotMask 26: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpNe 26: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLe 26: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLt 26: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 26: [ RUN ] Simd4FloatingpointTest.andB 26: [ OK ] Simd4FloatingpointTest.andB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.orB 26: [ OK ] Simd4FloatingpointTest.orB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.anyTrue 26: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 26: [ RUN ] Simd4FloatingpointTest.blend 26: [ OK ] Simd4FloatingpointTest.blend (0 ms) 26: [ RUN ] Simd4FloatingpointTest.reduce 26: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 26: [ RUN ] Simd4FloatingpointTest.dotProduct 26: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 26: [ RUN ] Simd4FloatingpointTest.transpose 26: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 26: [----------] 32 tests from Simd4FloatingpointTest (1 ms total) 26: 26: [----------] 1 test from Simd4VectorOperationsTest 26: [ RUN ] Simd4VectorOperationsTest.norm2 26: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 26: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 26: 26: [----------] 2 tests from Simd4MathTest 26: [ RUN ] Simd4MathTest.invsqrt 26: [ OK ] Simd4MathTest.invsqrt (0 ms) 26: [ RUN ] Simd4MathTest.invsqrtSingleaccuracy 26: [ OK ] Simd4MathTest.invsqrtSingleaccuracy (1 ms) 26: [----------] 2 tests from Simd4MathTest (1 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (2 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 277 tests from 22 test cases ran. (70 ms total) 26: [ PASSED ] 277 tests. 26/40 Test #26: SimdUnitTests .................... Passed 0.10 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/basic/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.02 sec test 28 Start 28: GmxAnaTest 28: Test command: /build/gromacs-2019.1/build/basic/bin/gmxana-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GmxAnaTest.xml" 28: Test timeout computed to be: 600 28: [==========] Running 26 tests from 5 test cases. 28: [----------] Global test environment set-up. 28: [----------] 5 tests from Entropy 28: [ RUN ] Entropy.Schlitter_300_NoLinear 28: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms) 28: [ RUN ] Entropy.Schlitter_300_Linear 28: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_Linear 28: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 28: [----------] 5 tests from Entropy (1 ms total) 28: 28: [----------] 3 tests from MsdTest 28: [ RUN ] MsdTest.threeDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.threeDimensionalDiffusion (2 ms) 28: [ RUN ] MsdTest.twoDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.twoDimensionalDiffusion (1 ms) 28: [ RUN ] MsdTest.oneDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.oneDimensionalDiffusion (2 ms) 28: [----------] 3 tests from MsdTest (5 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: trr version: GMX_trn_file (single precision) 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (7 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (2 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (19 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (9 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (4 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (2 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (24 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (5 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (1 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (11 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 26 tests from 5 test cases ran. (60 ms total) 28: [ PASSED ] 26 tests. 28/40 Test #28: GmxAnaTest ....................... Passed 0.08 sec test 29 Start 29: GmxPreprocessTests 29: Test command: /build/gromacs-2019.1/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/GmxPreprocessTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 26 tests from 4 test cases. 29: [----------] Global test environment set-up. 29: [----------] 4 tests from GenconfTest 29: [ RUN ] GenconfTest.nbox_Works 29: [ OK ] GenconfTest.nbox_Works (1 ms) 29: [ RUN ] GenconfTest.nbox_norenumber_Works 29: [ OK ] GenconfTest.nbox_norenumber_Works (1 ms) 29: [ RUN ] GenconfTest.nbox_dist_Works 29: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 29: [ RUN ] GenconfTest.nbox_rot_Works 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: [ OK ] GenconfTest.nbox_rot_Works (2 ms) 29: [----------] 4 tests from GenconfTest (5 ms total) 29: 29: [----------] 5 tests from InsertMoleculesTest 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: 29: Added 1 molecules (out of 1 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 29: 29: Output configuration contains 8 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (3 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 success (now 6 atoms)! 29: Try 4 success (now 8 atoms)! 29: Try 5 success (now 10 atoms)! 29: 29: Added 5 molecules (out of 5 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 29: 29: Output configuration contains 10 atoms in 10 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (2 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: Try 2 success (now 10 atoms)! 29: 29: Added 2 molecules (out of 2 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 29: 29: Output configuration contains 10 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (6 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 650 atoms)! 29: Try 2 success (now 652 atoms)! 29: Try 3 success (now 654 atoms)! 29: Try 4 success (now 656 atoms)! 29: 29: Added 4 molecules (out of 4 requested) 29: Replaced 8 residues (24 atoms) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 29: 29: Output configuration contains 632 atoms in 212 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (13 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Read 4 positions from file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 29: 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: 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) 29: Try 13 success (now 6 atoms)! 29: 29: Added 3 molecules (out of 4 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 29: 29: Output configuration contains 6 atoms in 3 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) 29: [----------] 5 tests from InsertMoleculesTest (28 ms total) 29: 29: [----------] 12 tests from GetIrTest 29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: Ignoring obsolete mdp entry 'title' 29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) 29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme 29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (4 ms) 29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (3 ms) 29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (4 ms) 29: [ RUN ] GetIrTest.EmptyInputWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.EmptyInputWorks (4 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricField 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricField (3 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (4 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (4 ms) 29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys 29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (7 ms) 29: [ RUN ] GetIrTest.ImplicitSolventNoWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ImplicitSolventNoWorks (4 ms) 29: [ RUN ] GetIrTest.ImplicitSolventYesWorks 29: [ OK ] GetIrTest.ImplicitSolventYesWorks (7 ms) 29: [ RUN ] GetIrTest.HandlesMimic 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]: 29: /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.HandlesMimic (4 ms) 29: [----------] 12 tests from GetIrTest (52 ms total) 29: 29: [----------] 5 tests from SolvateTest 29: [ RUN ] SolvateTest.cs_box_Works 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 1x1x1 boxes 29: Solvent box contains 270 atoms in 90 residues 29: Removed 129 solvent atoms due to solvent-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 47 residues 29: Generated solvent containing 141 atoms in 47 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 29: 29: Output configuration contains 141 atoms in 47 residues 29: Volume : 1.331 (nm^3) 29: Density : 1056.36 (g/l) 29: Number of solvent molecules: 47 29: 29: [ OK ] SolvateTest.cs_box_Works (14 ms) 29: [ RUN ] SolvateTest.cs_cp_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.777 (g/l) 29: Number of solvent molecules: 886 29: 29: [ OK ] SolvateTest.cs_cp_Works (61 ms) 29: [ RUN ] SolvateTest.cs_cp_p_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.777 (g/l) 29: Number of solvent molecules: 886 29: 29: Processing topology 29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top) 29: [ OK ] SolvateTest.cs_cp_p_Works (59 ms) 29: [ RUN ] SolvateTest.shell_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 1902 solvent atoms more than 1.000000 nm from solute. 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 252 residues 29: Generated solvent containing 756 atoms in 252 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 29: 29: Output configuration contains 762 atoms in 254 residues 29: Volume : 27.2709 (nm^3) 29: Density : 279.3 (g/l) 29: Number of solvent molecules: 252 29: 29: [ OK ] SolvateTest.shell_Works (32 ms) 29: [ RUN ] SolvateTest.update_Topology_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 3x3x3 boxes 29: Solvent box contains 14952 atoms in 4984 residues 29: Removed 2787 solvent atoms due to solvent-solvent overlap 29: Removed 30 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 2 different molecule types: 29: HOH ( 3 atoms): 1876 residues 29: SOL ( 3 atoms): 2169 residues 29: Generated solvent containing 0 atoms in 0 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 29: 29: Output configuration contains 12141 atoms in 4047 residues 29: Volume : 125 (nm^3) 29: Density : 968.963 (g/l) 29: Number of solvent molecules: 4045 29: 29: Processing topology 29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: [ OK ] SolvateTest.update_Topology_Works (228 ms) 29: [----------] 5 tests from SolvateTest (396 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 26 tests from 4 test cases ran. (481 ms total) 29: [ PASSED ] 26 tests. 29/40 Test #29: GmxPreprocessTests ............... Passed 0.50 sec test 30 Start 30: Pdb2gmxTest 30: Test command: /build/gromacs-2019.1/build/basic/bin/pdb2gmx-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/Pdb2gmxTest.xml" 30: Test timeout computed to be: 480 30: [==========] Running 80 tests from 6 test cases. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (493 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (536 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (495 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (445 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (528 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (585 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (562 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (500 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (497 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (553 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (485 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (441 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (516 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (582 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (534 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (479 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (477 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (542 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (514 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (479 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (548 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (618 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (561 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (502 ms) 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (12473 ms total) 30: 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (257 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (304 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (260 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (242 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (273 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (324 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (273 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (249 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (257 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (301 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (259 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (234 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (267 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (303 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (265 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (241 ms) 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (4310 ms total) 30: 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (255 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (296 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (251 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (235 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (267 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (305 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (265 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (240 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (246 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (299 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (258 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (236 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (263 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (314 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (272 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (254 ms) 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (4257 ms total) 30: 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (476 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (535 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (484 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (425 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (528 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (583 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (522 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (466 ms) 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (4020 ms total) 30: 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (471 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (532 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (475 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (435 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (512 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (559 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (507 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (460 ms) 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3952 ms total) 30: 30: [----------] 8 tests from ChainSep/Pdb2gmxTest 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (478 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 7 acceptors were found. 30: There are 7 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS8 30: NE223 30: MET12 SD55 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 125, now 125 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 317 pairs 30: Before cleaning: 322 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 5 cmap torsion pairs 30: There are 322 dihedrals, 19 impropers, 227 angles 30: 314 pairs, 125 bonds and 0 virtual sites 30: Total mass 846.083 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 7 58 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (58 atoms, 7 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 7 residues with 124 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 124 atoms 7 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (81 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (471 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 12 acceptors were found. 30: There are 13 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 30: SG9 30: HIS8 NE251 1.055 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 115, now 115 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 288 pairs 30: Before cleaning: 293 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 6 cmap torsion pairs 30: There are 293 dihedrals, 23 impropers, 203 angles 30: 285 pairs, 115 bonds and 0 virtual sites 30: Total mass 888.952 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 8 61 30: 2 'B' 3 25 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (61 atoms, 8 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 8 residues with 114 atoms 30: Chain time... 30: Processing chain 2 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 114 atoms 8 residues 30: Including chain 2 in system: 61 atoms 3 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (78 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 260, now 260 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 650 pairs 30: Before cleaning: 660 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 8 cmap torsion pairs 30: There are 660 dihedrals, 45 impropers, 466 angles 30: 647 pairs, 260 bonds and 0 virtual sites 30: Total mass 1900.162 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: 30: Merged chains into joint molecule definitions at 3 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 261 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (472 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 6 donors and 4 acceptors were found. 30: There are 3 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 67, now 67 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 164 pairs 30: Before cleaning: 169 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 169 dihedrals, 13 impropers, 118 angles 30: 161 pairs, 67 bonds and 0 virtual sites 30: Total mass 472.547 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 261 atoms and 16 residues 30: Total mass in system 1900.162 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 30: They will be treated as separate chains unless you reorder your file. 30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 4 33 30: 3 'B' 3 25 30: 4 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (33 atoms, 4 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 66 atoms 30: Chain time... 30: Processing chain 3 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 4 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 66 atoms 4 residues 30: Including chain 3 in system: 61 atoms 3 residues 30: Including chain 4 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (81 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 256, now 256 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 652 pairs 30: Before cleaning: 662 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 12 cmap torsion pairs 30: There are 662 dihedrals, 47 impropers, 460 angles 30: 649 pairs, 256 bonds and 0 virtual sites 30: Total mass 1864.131 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: 30: Merged chains into joint molecule definitions at 1 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (457 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 14 donors and 15 acceptors were found. 30: There are 20 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 173, now 173 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 441 pairs 30: Before cleaning: 446 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 9 cmap torsion pairs 30: There are 446 dihedrals, 29 impropers, 312 angles 30: 438 pairs, 173 bonds and 0 virtual sites 30: Total mass 1262.488 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 255 atoms and 16 residues 30: Total mass in system 1864.131 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 11 86 30: 2 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (86 atoms, 11 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 11 residues with 172 atoms 30: Chain time... 30: Processing chain 2 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 172 atoms 11 residues 30: Including chain 2 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (78 ms) 30: [----------] 8 tests from ChainSep/Pdb2gmxTest (2196 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 80 tests from 6 test cases ran. (31208 ms total) 30: [ PASSED ] 80 tests. 30/40 Test #30: Pdb2gmxTest ...................... Passed 31.25 sec test 31 Start 31: CorrelationsTest 31: Test command: /build/gromacs-2019.1/build/basic/bin/correlations-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/CorrelationsTest.xml" 31: Test timeout computed to be: 30 31: [==========] Running 11 tests from 2 test cases. 31: [----------] Global test environment set-up. 31: [----------] 10 tests from AutocorrTest 31: [ RUN ] AutocorrTest.EacNormal 31: [ OK ] AutocorrTest.EacNormal (32 ms) 31: [ RUN ] AutocorrTest.EacNoNormalize 31: [ OK ] AutocorrTest.EacNoNormalize (16 ms) 31: [ RUN ] AutocorrTest.EacCos 31: [ OK ] AutocorrTest.EacCos (40 ms) 31: [ RUN ] AutocorrTest.EacVector 31: [ OK ] AutocorrTest.EacVector (60 ms) 31: [ RUN ] AutocorrTest.EacRcross 31: [ OK ] AutocorrTest.EacRcross (2 ms) 31: [ RUN ] AutocorrTest.EacP0 31: [ OK ] AutocorrTest.EacP0 (66 ms) 31: [ RUN ] AutocorrTest.EacP1 31: [ OK ] AutocorrTest.EacP1 (55 ms) 31: [ RUN ] AutocorrTest.EacP2 31: [ OK ] AutocorrTest.EacP2 (108 ms) 31: [ RUN ] AutocorrTest.EacP3 31: [ OK ] AutocorrTest.EacP3 (8 ms) 31: [ RUN ] AutocorrTest.EacP4 31: [ OK ] AutocorrTest.EacP4 (35 ms) 31: [----------] 10 tests from AutocorrTest (424 ms total) 31: 31: [----------] 1 test from ManyAutocorrelationTest 31: [ RUN ] ManyAutocorrelationTest.Empty 31: [ OK ] ManyAutocorrelationTest.Empty (1 ms) 31: [----------] 1 test from ManyAutocorrelationTest (1 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 11 tests from 2 test cases ran. (431 ms total) 31: [ PASSED ] 11 tests. 31/40 Test #31: CorrelationsTest ................. Passed 0.45 sec test 32 Start 32: AnalysisDataUnitTests 32: Test command: /build/gromacs-2019.1/build/basic/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml" 32: Test timeout computed to be: 30 32: [==========] Running 69 tests from 14 test cases. 32: [----------] Global test environment set-up. 32: [----------] 3 tests from AnalysisDataInitializationTest 32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 32: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/0 (7 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/1 (7 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/2 (8 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/3 (9 ms total) 32: 32: [----------] 4 tests from AnalysisArrayDataTest 32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisArrayDataTest.StorageWorks 32: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (1 ms) 32: [----------] 4 tests from AnalysisArrayDataTest (2 ms total) 32: 32: [----------] 6 tests from AverageModuleTest 32: [ RUN ] AverageModuleTest.BasicTest 32: [ OK ] AverageModuleTest.BasicTest (1 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipointData 32: [ OK ] AverageModuleTest.HandlesMultipointData (1 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (2 ms) 32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (2 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeXAxis 32: [ OK ] AverageModuleTest.CanCustomizeXAxis (1 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 32: [----------] 6 tests from AverageModuleTest (8 ms total) 32: 32: [----------] 2 tests from FrameAverageModuleTest 32: [ RUN ] FrameAverageModuleTest.BasicTest 32: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (1 ms) 32: [----------] 2 tests from FrameAverageModuleTest (3 ms total) 32: 32: [----------] 7 tests from AnalysisHistogramSettingsTest 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 32: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 32: 32: [----------] 2 tests from SimpleHistogramModuleTest 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (2 ms) 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 32: [----------] 2 tests from SimpleHistogramModuleTest (4 ms total) 32: 32: [----------] 3 tests from WeightedHistogramModuleTest 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (2 ms) 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (3 ms) 32: [----------] 3 tests from WeightedHistogramModuleTest (7 ms total) 32: 32: [----------] 3 tests from BinAverageModuleTest 32: [ RUN ] BinAverageModuleTest.ComputesCorrectly 32: [ OK ] BinAverageModuleTest.ComputesCorrectly (1 ms) 32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (2 ms) 32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (2 ms) 32: [----------] 3 tests from BinAverageModuleTest (5 ms total) 32: 32: [----------] 4 tests from AbstractAverageHistogramTest 32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (2 ms) 32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (2 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (1 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (2 ms) 32: [----------] 4 tests from AbstractAverageHistogramTest (8 ms total) 32: 32: [----------] 3 tests from LifetimeModuleTest 32: [ RUN ] LifetimeModuleTest.BasicTest 32: [ OK ] LifetimeModuleTest.BasicTest (1 ms) 32: [ RUN ] LifetimeModuleTest.CumulativeTest 32: [ OK ] LifetimeModuleTest.CumulativeTest (2 ms) 32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (1 ms) 32: [----------] 3 tests from LifetimeModuleTest (4 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 69 tests from 14 test cases ran. (72 ms total) 32: [ PASSED ] 69 tests. 32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.09 sec test 33 Start 33: SelectionUnitTests 33: Test command: /build/gromacs-2019.1/build/basic/bin/selection-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/SelectionUnitTests.xml" 33: Test timeout computed to be: 30 33: [==========] Running 190 tests from 10 test cases. 33: [----------] Global test environment set-up. 33: [----------] 1 test from IndexGroupTest 33: [ RUN ] IndexGroupTest.RemovesDuplicates 33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 33: [----------] 1 test from IndexGroupTest (0 ms total) 33: 33: [----------] 15 tests from IndexBlockTest 33: [ RUN ] IndexBlockTest.CreatesUnknownBlock 33: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesAtomBlock 33: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlock 33: [ OK ] IndexBlockTest.CreatesResidueBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock 33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (0 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (0 ms) 33: [ RUN ] IndexBlockTest.CreatesSingleBlock 33: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 33: [----------] 15 tests from IndexBlockTest (2 ms total) 33: 33: [----------] 11 tests from IndexMapTest 33: [ RUN ] IndexMapTest.InitializesAtomBlock 33: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (1 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (1 ms) 33: [ RUN ] IndexMapTest.InitializesMoleculeBlock 33: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 33: [ RUN ] IndexMapTest.MapsSingleBlock 33: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocks 33: [ OK ] IndexMapTest.MapsResidueBlocks (4 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 33: [ RUN ] IndexMapTest.HandlesMultipleRequests 33: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 33: [----------] 11 tests from IndexMapTest (8 ms total) 33: 33: [----------] 15 tests from NeighborhoodSearchTest 33: [ RUN ] NeighborhoodSearchTest.SimpleSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSearch (26 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (28 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchBox 33: [ OK ] NeighborhoodSearchTest.GridSearchBox (3 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (16 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (7 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (4 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (3 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (73 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (6 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 33: [----------] 15 tests from NeighborhoodSearchTest (168 ms total) 33: 33: [----------] 12 tests from PositionCalculationTest 33: [ RUN ] PositionCalculationTest.ComputesAtomPositions 33: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionMask 33: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms) 33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 33: [----------] 12 tests from PositionCalculationTest (5 ms total) 33: 33: [----------] 30 tests from SelectionCollectionTest 33: [ RUN ] SelectionCollectionTest.HandlesNoSelections 33: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) 33: [----------] 30 tests from SelectionCollectionTest (19 ms total) 33: 33: [----------] 14 tests from SelectionCollectionInteractiveTest 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (0 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (0 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (0 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 33: [----------] 14 tests from SelectionCollectionInteractiveTest (11 ms total) 33: 33: [----------] 66 tests from SelectionCollectionDataTest 33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (0 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResnr 33: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesChain 33: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMass 33: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCharge 33: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBeta 33: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResname 33: [ OK ] SelectionCollectionDataTest.HandlesResname (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (6 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (0 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (2 ms) 33: [----------] 66 tests from SelectionCollectionDataTest (94 ms total) 33: 33: [----------] 17 tests from SelectionOptionTest 33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (0 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptySelections 33: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelections 33: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesAdjuster 33: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms) 33: [----------] 17 tests from SelectionOptionTest (8 ms total) 33: 33: [----------] 9 tests from SelectionFileOptionTest 33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (0 ms) 33: [----------] 9 tests from SelectionFileOptionTest (4 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 190 tests from 10 test cases ran. (319 ms total) 33: [ PASSED ] 190 tests. 33/40 Test #33: SelectionUnitTests ............... Passed 0.34 sec test 34 Start 34: TrajectoryAnalysisUnitTests 34: Test command: /build/gromacs-2019.1/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 34: Test timeout computed to be: 30 34: [==========] Running 74 tests from 14 test cases. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from ClustsizeTest 34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 2, cmax: 4, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (3 ms) 34: [ RUN ] ClustsizeTest.NoMolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 1, cmax: 6, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (2 ms) 34: [ RUN ] ClustsizeTest.MolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (7 ms) 34: [ RUN ] ClustsizeTest.MolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 1, cmax: 6, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (3 ms) 34: [ RUN ] ClustsizeTest.MolCSize 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolCSize (3 ms) 34: [----------] 5 tests from ClustsizeTest (18 ms total) 34: 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (2 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (5 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (9 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (0 ms) 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (16 ms total) 34: 34: [----------] 11 tests from AngleModuleTest 34: [ RUN ] AngleModuleTest.ComputesSimpleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesSimpleAngles (6 ms) 34: [ RUN ] AngleModuleTest.ComputesDihedrals 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesDihedrals (5 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (5 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (6 ms) 34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (5 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (5 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 34: Reading frames from gro file 'Test system for different angles', 33 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (5 ms) 34: [ RUN ] AngleModuleTest.ComputesMultipleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesMultipleAngles (6 ms) 34: [ RUN ] AngleModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesDynamicSelections (5 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (5 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (5 ms) 34: [----------] 11 tests from AngleModuleTest (58 ms total) 34: 34: [----------] 3 tests from DistanceModuleTest 34: [ RUN ] DistanceModuleTest.ComputesDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: [ OK ] DistanceModuleTest.ComputesDistances (6 ms) 34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 34: Number of samples: 4 34: Average distance: 1.81066 nm 34: Standard deviation: 0.79289 nm 34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (7 ms) 34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2 and res_cog x < 2.8: 34: Number of samples: 3 34: Average distance: 1.72076 nm 34: Standard deviation: 1.24839 nm 34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (7 ms) 34: [----------] 3 tests from DistanceModuleTest (21 ms total) 34: 34: [----------] 2 tests from FreeVolumeModuleTest 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for 40 particles. These were set to zero. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 13 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.02 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 34: Fractional free volume 0.194 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (186 ms) 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 17 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.48 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 34: Fractional free volume 0.200 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (185 ms) 34: [----------] 2 tests from FreeVolumeModuleTest (371 ms total) 34: 34: [----------] 7 tests from PairDistanceModuleTest 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (5 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (5 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (5 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (4 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (5 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (5 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (5 ms) 34: [----------] 7 tests from PairDistanceModuleTest (34 ms total) 34: 34: [----------] 5 tests from RdfModuleTest 34: [ RUN ] RdfModuleTest.BasicTest 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.BasicTest (38 ms) 34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (30 ms) 34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (38 ms) 34: [ RUN ] RdfModuleTest.CalculatesSurf 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesSurf (19 ms) 34: [ RUN ] RdfModuleTest.CalculatesXY 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesXY (44 ms) 34: [----------] 5 tests from RdfModuleTest (170 ms total) 34: 34: [----------] 5 tests from SasaModuleTest 34: [ RUN ] SasaModuleTest.BasicTest 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.BasicTest (19 ms) 34: [ RUN ] SasaModuleTest.HandlesSelectedResidues 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesSelectedResidues (11 ms) 34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (11 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (14 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (14 ms) 34: [----------] 5 tests from SasaModuleTest (73 ms total) 34: 34: [----------] 8 tests from SelectModuleTest 34: [ RUN ] SelectModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.BasicTest (8 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (7 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (8 ms) 34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (7 ms) 34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (7 ms) 34: [ RUN ] SelectModuleTest.NormalizesSizes 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.NormalizesSizes (5 ms) 34: [ RUN ] SelectModuleTest.WritesResidueNumbers 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueNumbers (5 ms) 34: [ RUN ] SelectModuleTest.WritesResidueIndices 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueIndices (4 ms) 34: [----------] 8 tests from SelectModuleTest (52 ms total) 34: 34: [----------] 10 tests from SurfaceAreaTest 34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (1 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (1 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints12 34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints32 34: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints42 34: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints122 34: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 34: [ RUN ] SurfaceAreaTest.Computes100Points 34: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (4 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (4 ms) 34: [----------] 10 tests from SurfaceAreaTest (16 ms total) 34: 34: [----------] 4 tests from TopologyInformation 34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms) 34: [ RUN ] TopologyInformation.WorksWithGroFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithGroFile (5 ms) 34: [ RUN ] TopologyInformation.WorksWithPdbFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithPdbFile (5 ms) 34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 34: 34: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]: 34: /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 34: scheme was introduced, but the group scheme was still the default. The 34: default is now the Verlet scheme, so you will observe different behaviour. 34: 34: 34: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: For a correct single-point energy evaluation with nsteps = 0, use 34: continuation = yes to avoid constraining the input coordinates. 34: 34: Setting the LD random seed to 824489530 34: Generated 330891 of the 330891 non-bonded parameter combinations 34: Generating 1-4 interactions: fudge = 0.5 34: Generated 330891 of the 330891 1-4 parameter combinations 34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 34: 34: NOTE 3 [file lysozyme.top, line 1465]: 34: System has non-zero total charge: 2.000000 34: Total charge should normally be an integer. See 34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 34: for discussion on how close it should be to an integer. 34: 34: 34: 34: Removing all charge groups because cutoff-scheme=Verlet 34: Number of degrees of freedom in T-Coupling group rest is 465.00 34: 34: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: NVE simulation with an initial temperature of zero: will use a Verlet 34: buffer of 10%. Check your energy drift! 34: 34: 34: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: You are using a plain Coulomb cut-off, which might produce artifacts. 34: You might want to consider using PME electrostatics. 34: 34: 34: 34: There were 5 notes 34: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (single precision) 34: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (single precision) 34: Analysing residue names: 34: There are: 10 Protein residues 34: Analysing Protein... 34: This run will generate roughly 0 Mb of data 34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (347 ms) 34: [----------] 4 tests from TopologyInformation (357 ms total) 34: 34: [----------] 4 tests from TrajectoryModuleTest 34: [ RUN ] TrajectoryModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.BasicTest (7 ms) 34: [ RUN ] TrajectoryModuleTest.PlotsXOnly 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.PlotsXOnly (6 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (5 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoForces 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoForces (5 ms) 34: [----------] 4 tests from TrajectoryModuleTest (23 ms total) 34: 34: [----------] 5 tests from UnionFinderTest 34: [ RUN ] UnionFinderTest.WorksEmpty 34: [ OK ] UnionFinderTest.WorksEmpty (1 ms) 34: [ RUN ] UnionFinderTest.BasicMerges 34: [ OK ] UnionFinderTest.BasicMerges (0 ms) 34: [ RUN ] UnionFinderTest.LargerMerges 34: [ OK ] UnionFinderTest.LargerMerges (0 ms) 34: [ RUN ] UnionFinderTest.LongRightMerge 34: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 34: [ RUN ] UnionFinderTest.LongLeftMerge 34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 34: [----------] 5 tests from UnionFinderTest (1 ms total) 34: 34: [----------] 1 test from MappedUnionFinderTest 34: [ RUN ] MappedUnionFinderTest.BasicMerges 34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 34: [----------] 1 test from MappedUnionFinderTest (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 74 tests from 14 test cases ran. (1211 ms total) 34: [ PASSED ] 74 tests. 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 1.23 sec test 35 Start 35: EnergyAnalysisUnitTests 35: Test command: /build/gromacs-2019.1/build/basic/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 7 tests from 4 test cases. 35: [----------] Global test environment set-up. 35: [----------] 1 test from DhdlTest 35: [ RUN ] DhdlTest.ExtractDhdl 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 35: Note: file tpx version 110, software tpx version 116 35: 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 35: 35: 35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-2019.1/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 35: [ OK ] DhdlTest.ExtractDhdl (18 ms) 35: [----------] 1 test from DhdlTest (19 ms total) 35: 35: [----------] 1 test from OriresTest 35: [ RUN ] OriresTest.ExtractOrires 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 35: Note: file tpx version 111, software tpx version 116 35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 35: End your selection with 0 35: Selecting all 7 orientation restraints 35: 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 35: [ OK ] OriresTest.ExtractOrires (15 ms) 35: [----------] 1 test from OriresTest (16 ms total) 35: 35: [----------] 3 tests from EnergyTest 35: [ RUN ] EnergyTest.ExtractEnergy 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: [ OK ] EnergyTest.ExtractEnergy (4 ms) 35: [ RUN ] EnergyTest.ExtractEnergyByNumber 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Pres. DC -268.49 3 8.52175 13.2804 (bar) 35: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) 35: [ RUN ] EnergyTest.ExtractEnergyMixed 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: [ OK ] EnergyTest.ExtractEnergyMixed (10 ms) 35: [----------] 3 tests from EnergyTest (19 ms total) 35: 35: [----------] 2 tests from ViscosityTest 35: [ RUN ] ViscosityTest.EinsteinViscosity 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosity (108 ms) 35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (75 ms) 35: [----------] 2 tests from ViscosityTest (184 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 7 tests from 4 test cases ran. (238 ms total) 35: [ PASSED ] 7 tests. 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.26 sec test 36 Start 36: ToolUnitTests 36: Test command: /build/gromacs-2019.1/build/basic/bin/tool-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/ToolUnitTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 4 tests from 1 test case. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ReportMethodsTest 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectInformation 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to 568289616 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.1 (single precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: [ OK ] ReportMethodsTest.WritesCorrectInformation (386 ms) 36: [ RUN ] ReportMethodsTest.ToolEndToEndTest 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to 1159543049 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.1 (single precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: section: Methods 36: subsection: Simulation system 36: A system of 1 molecules (156 atoms) was simulated. 36: 36: subsection: Simulation settings 36: A total of 0 ns were simulated with a time step of 1 fs. 36: Neighbor searching was performed every 10 steps. 36: The Cut-off algorithm was used for electrostatic interactions. 36: with a cut-off of 1 nm. 36: A single cut-off of 1.1 nm was used for Van der Waals interactions. 36: [ OK ] ReportMethodsTest.ToolEndToEndTest (375 ms) 36: [----------] 4 tests from ReportMethodsTest (761 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 4 tests from 1 test case ran. (761 ms total) 36: [ PASSED ] 4 tests. 36/40 Test #36: ToolUnitTests .................... Passed 0.78 sec test 37 Start 37: MdrunTests 37: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunTests.xml" 37: Test timeout computed to be: 600 37: [==========] Running 29 tests from 11 test cases. 37: [----------] Global test environment set-up. 37: [----------] 1 test from GromppTest 37: [ RUN ] GromppTest.EmptyMdpFileWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -999089724 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] GromppTest.EmptyMdpFileWorks (48 ms) 37: [----------] 1 test from GromppTest (48 ms total) 37: 37: [----------] 1 test from ImdTest 37: [ RUN ] ImdTest.ImdCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to 1558045135 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD). 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 50, rlist from 1.121 to 1.344 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: IMD: Enabled. This simulation will accept incoming IMD connections. 37: IMD: You chose a port number < 1. Will automatically assign a free port. 37: IMD: Pulling from IMD remote is enabled (-imdpull). 37: IMD: Turning on IMD - port for incoming requests is 0. 37: IMD: Setting up incoming socket. 37: IMD: Listening for IMD connection on port 39491. 37: IMD: -imdwait not set, starting simulation. 37: starting mdrun 'spc2' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 69 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.015 0.008 198.0 37: (ns/day) (hour/ns) 37: Performance: 132.860 0.181 37: [ OK ] ImdTest.ImdCanRun (79 ms) 37: [----------] 1 test from ImdTest (79 ms total) 37: 37: [----------] 2 tests from PmeTest 37: [ RUN ] PmeTest.ReproducesEnergies 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -362500564 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.055 0.028 199.4 37: (ns/day) (hour/ns) 37: Performance: 65.565 0.366 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 37: 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/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.059 0.029 199.5 37: (ns/day) (hour/ns) 37: Performance: 61.580 0.390 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 37: 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/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.055 0.028 199.3 37: (ns/day) (hour/ns) 37: Performance: 65.409 0.367 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 37: 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 ] PmeTest.ReproducesEnergies (10175 ms) 37: [ RUN ] PmeTest.ScalesTheBox 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1904877146 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Searching the wall atom type(s) 37: Number of degrees of freedom in T-Coupling group rest is 13.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: NVE simulation: will use the initial temperature of 966.268 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 0 steps, 0.0 ps. 37: 37: NOTE: 12 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 194.5 37: (ns/day) (hour/ns) 37: Performance: 17.462 1.374 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 37: This run will generate roughly 0 Mb of data 37: [ OK ] PmeTest.ScalesTheBox (32081 ms) 37: [----------] 2 tests from PmeTest (42256 ms total) 37: 37: [----------] 1 test from CompelTest 37: [ RUN ] CompelTest.SwapCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to -1546668422 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 1 bonded neighbours molecule type 'NA' 37: Excluding 1 bonded neighbours molecule type 'CL' 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Split0 group 'Ch0' contains 83 atoms. 37: Split1 group 'Ch1' contains 83 atoms. 37: Solvent group 'SOL' contains 11931 atoms. 37: Swap group 'NA+' contains 19 atoms. 37: Swap group 'CL-' contains 19 atoms. 37: Number of degrees of freedom in T-Coupling group System is 27869.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (single precision) 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: SWAP: Determining initial numbers of ions per compartment. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 1 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 35 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.823 0.412 199.9 37: (ns/day) (hour/ns) 37: Performance: 3.148 7.625 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Copying channel fluxes from checkpoint file data 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: NOTE: 25 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.571 0.285 199.9 37: (ns/day) (hour/ns) 37: Performance: 4.540 5.287 37: [ OK ] CompelTest.SwapCanRun (1345 ms) 37: [----------] 1 test from CompelTest (1345 ms total) 37: 37: [----------] 6 tests from BondedInteractionsTest 37: [ RUN ] BondedInteractionsTest.NormalBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -153886915 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 18 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.4 37: (ns/day) (hour/ns) 37: Performance: 200.992 0.119 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalBondWorks (14 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1358110320 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 191.7 37: (ns/day) (hour/ns) 37: Performance: 124.918 0.192 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (11 ms) 37: [ RUN ] BondedInteractionsTest.NormalAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 740814072 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 16 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.3 37: (ns/day) (hour/ns) 37: Performance: 221.644 0.108 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalAngleWorks (9 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -591171436 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 17 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 187.8 37: (ns/day) (hour/ns) 37: Performance: 221.103 0.109 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (10 ms) 37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1972013051 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 11 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 193.1 37: (ns/day) (hour/ns) 37: Performance: 106.117 0.226 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (9 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1164245216 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 23 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 189.8 37: (ns/day) (hour/ns) 37: Performance: 159.361 0.151 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (16 ms) 37: [----------] 6 tests from BondedInteractionsTest (69 ms total) 37: 37: [----------] 2 tests from MdrunTerminationTest 37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1461319412 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: NOTE: 58 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.006 0.003 195.2 37: (ns/day) (hour/ns) 37: Performance: 55.722 0.431 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 189.9 37: (ns/day) (hour/ns) 37: Performance: 204.239 0.118 37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (18 ms) 37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1001848293 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 1, rlist from 1.024 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 2: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.004 0.002 193.3 37: (ns/day) (hour/ns) 37: Performance: 162.670 0.148 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (single precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 5 steps, 0.0 ps (continuing from step 3, 0.0 ps). 37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.001 195.2 37: (ns/day) (hour/ns) 37: Performance: 198.171 0.121 37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (17 ms) 37: [----------] 2 tests from MdrunTerminationTest (35 ms total) 37: 37: [----------] 4 tests from MimicTest 37: [ RUN ] MimicTest.OneQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 249477040 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 24 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.8 37: (ns/day) (hour/ns) 37: Performance: 181.103 0.133 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.OneQuantumMol (10 ms) 37: [ RUN ] MimicTest.AllQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 333902783 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 92 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.011 0.005 198.6 37: (ns/day) (hour/ns) 37: Performance: 16.343 1.469 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.AllQuantumMol (15 ms) 37: [ RUN ] MimicTest.TwoQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1933742016 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 94 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.013 0.006 198.8 37: (ns/day) (hour/ns) 37: Performance: 13.506 1.777 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.TwoQuantumMol (16 ms) 37: [ RUN ] MimicTest.BondCuts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1582805337 37: Generated 2211 of the 2211 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 2211 of the 2211 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 66.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: NVE simulation: will use the initial temperature of 300.368 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 37: 37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.004 0.002 196.7 37: (ns/day) (hour/ns) 37: Performance: 39.592 0.606 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.BondCuts (29 ms) 37: [----------] 4 tests from MimicTest (70 ms total) 37: 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 37: Setting the LD random seed to -1322029493 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.012 0.006 197.2 37: (ns/day) (hour/ns) 37: Performance: 27.880 0.861 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (16 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 37: Setting the LD random seed to -1987879968 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 191.2 37: (ns/day) (hour/ns) 37: Performance: 98.757 0.243 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (12 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 37: Setting the LD random seed to 1325585592 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 191.5 37: (ns/day) (hour/ns) 37: Performance: 98.142 0.245 37: Reading frame 0 time 0.000 37: # Atoms 3 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (12 ms) 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (40 ms total) 37: 37: [----------] 3 tests from Checking/InitialConstraintsTest 37: [ RUN ] Checking/InitialConstraintsTest.Works/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 2034292669 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 14 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 191.2 37: (ns/day) (hour/ns) 37: Performance: 98.315 0.244 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (42 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -175983217 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 72 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.011 0.006 197.3 37: (ns/day) (hour/ns) 37: Performance: 29.920 0.802 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (43 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: Integrator method md-vv-avek is implemented primarily for validation 37: purposes; for molecular dynamics, you should probably be using md or md-vv 37: 37: Setting the LD random seed to 869555440 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.1 (single precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 13 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.065 0.033 199.4 37: (ns/day) (hour/ns) 37: Performance: 5.291 4.536 37: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (75 ms) 37: [----------] 3 tests from Checking/InitialConstraintsTest (160 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/Trajectories 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1152544163 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.108 0.054 199.7 37: (ns/day) (hour/ns) 37: Performance: 11.192 2.144 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (111 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1942664790 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.100 0.050 199.6 37: (ns/day) (hour/ns) 37: Performance: 12.044 1.993 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (98 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1729794384 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.099 0.050 199.6 37: (ns/day) (hour/ns) 37: Performance: 12.168 1.972 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (99 ms) 37: [----------] 3 tests from MdrunCanWrite/Trajectories (309 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 952734545 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 10 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.051 0.026 199.2 37: (ns/day) (hour/ns) 37: Performance: 10.120 2.372 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (74 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1030158603 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 10 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.051 0.025 199.2 37: (ns/day) (hour/ns) 37: Performance: 10.220 2.348 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (73 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1769870420 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.1 (single precision) 37: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 10 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.051 0.025 199.1 37: (ns/day) (hour/ns) 37: Performance: 10.192 2.355 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (74 ms) 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (221 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 29 tests from 11 test cases ran. (44633 ms total) 37: [ PASSED ] 29 tests. 37/40 Test #37: MdrunTests ....................... Passed 44.67 sec test 38 Start 38: MdrunNonIntegratorTests 38: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml" 38: Test timeout computed to be: 600 38: [==========] Running 57 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -4.7990940e+01 38: Maximum force = 1.8629752e+02 on atom 13 38: Norm of force = 8.7721851e+01 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (392 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 3.02331e+02 on atom 3 38: F-Norm = 1.18024e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -5.5862331e+01 38: Maximum force = 4.2726447e+02 on atom 13 38: Norm of force = 1.8452602e+02 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (342 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.1937726e+02 38: Maximum force = 9.9988691e+03 on atom 9 38: Norm of force = 4.6167015e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 38: 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 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (228 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: 38: NOTE 3 [file glycine_vacuo.top, line 12]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41575e+04 on atom 10 38: F-Norm = 1.18451e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.5174414e+02 38: Maximum force = 7.4208760e+03 on atom 9 38: Norm of force = 3.5692977e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 38: 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 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (237 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.5698456e+02 38: Maximum force = 4.5702225e+02 on atom 17 38: Norm of force = 1.8327095e+02 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 38: 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 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (149 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: 38: NOTE 4 [file unknown]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 1.06799e+03 on atom 28 38: F-Norm = 4.26914e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.6941235e+02 38: Maximum force = 2.1838159e+02 on atom 17 38: Norm of force = 7.9235189e+01 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 38: 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 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (99 ms) 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1447 ms total) 38: 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents converged to Fmax < 10 in 1 steps 38: Potential Energy = -9.7425687e-01 38: Maximum force = 4.0132279e+00 on atom 1 38: Norm of force = 1.6383933e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (61 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.9064195e-01 38: Maximum force = 2.5781672e+00 on atom 1 38: Norm of force = 1.0525324e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (66 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.9064195e-01 38: Maximum force = 2.5781672e+00 on atom 1 38: Norm of force = 1.0525324e+00 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (56 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.1939673e+02 38: Maximum force = 9.9704229e+03 on atom 9 38: Norm of force = 4.6227534e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (169 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.5625757e+02 38: Maximum force = 7.5018237e+03 on atom 9 38: Norm of force = 3.6139019e+03 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (182 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.8472457e+03 38: Maximum force = 2.1261648e+04 on atom 9 38: Norm of force = 1.0198873e+04 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (163 ms) 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (697 ms total) 38: 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 10 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 191.6 38: (ns/day) (hour/ns) 38: Performance: 841.611 0.029 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr' 38: 38: trr version: GMX_trn_file (single precision) 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 193.6 38: (ns/day) (hour/ns) 38: Performance: 1457.784 0.016 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (90 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 192.0 38: (ns/day) (hour/ns) 38: Performance: 778.147 0.031 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 193.1 38: (ns/day) (hour/ns) 38: Performance: 1385.649 0.017 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (79 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 192.0 38: (ns/day) (hour/ns) 38: Performance: 735.681 0.033 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 193.8 38: (ns/day) (hour/ns) 38: Performance: 1453.656 0.017 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (90 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 193.1 38: (ns/day) (hour/ns) 38: Performance: 597.710 0.040 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 22 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 193.1 38: (ns/day) (hour/ns) 38: Performance: 1497.835 0.016 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (121 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 191.9 38: (ns/day) (hour/ns) 38: Performance: 761.507 0.032 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 194.3 38: (ns/day) (hour/ns) 38: Performance: 1335.196 0.018 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (403 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 192.9 38: (ns/day) (hour/ns) 38: Performance: 648.279 0.037 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 193.7 38: (ns/day) (hour/ns) 38: Performance: 1360.555 0.018 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (386 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 191.7 38: (ns/day) (hour/ns) 38: Performance: 764.247 0.031 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 194.1 38: (ns/day) (hour/ns) 38: Performance: 1357.258 0.018 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (388 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 192.8 38: (ns/day) (hour/ns) 38: Performance: 646.646 0.037 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 194.0 38: (ns/day) (hour/ns) 38: Performance: 1300.252 0.018 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (390 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.007 0.004 195.0 38: (ns/day) (hour/ns) 38: Performance: 396.358 0.061 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.002 196.0 38: (ns/day) (hour/ns) 38: Performance: 853.859 0.028 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (116 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 51 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 197.7 38: (ns/day) (hour/ns) 38: Performance: 171.796 0.140 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 74 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 198.7 38: (ns/day) (hour/ns) 38: Performance: 246.276 0.097 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (142 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 195.3 38: (ns/day) (hour/ns) 38: Performance: 352.114 0.068 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 77 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.007 198.8 38: (ns/day) (hour/ns) 38: Performance: 219.927 0.109 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (160 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.9 38: (ns/day) (hour/ns) 38: Performance: 305.040 0.079 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 33 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 196.4 38: (ns/day) (hour/ns) 38: Performance: 699.035 0.034 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (134 ms) 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (2500 ms total) 38: 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 61 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.021 0.011 198.0 38: (ns/day) (hour/ns) 38: Performance: 139.487 0.172 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 79 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 198.4 38: (ns/day) (hour/ns) 38: Performance: 165.070 0.145 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (139 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 59 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.020 0.010 197.8 38: (ns/day) (hour/ns) 38: Performance: 146.385 0.164 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 59 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 196.8 38: (ns/day) (hour/ns) 38: Performance: 314.573 0.076 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (122 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 194.8 38: (ns/day) (hour/ns) 38: Performance: 326.285 0.074 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 194.4 38: (ns/day) (hour/ns) 38: Performance: 626.841 0.038 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (141 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 194.8 38: (ns/day) (hour/ns) 38: Performance: 339.670 0.071 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 64 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 197.3 38: (ns/day) (hour/ns) 38: Performance: 277.467 0.086 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (101 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.008 197.3 38: (ns/day) (hour/ns) 38: Performance: 174.210 0.138 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 67 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 197.6 38: (ns/day) (hour/ns) 38: Performance: 249.427 0.096 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (136 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 197.1 38: (ns/day) (hour/ns) 38: Performance: 169.391 0.142 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 77 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 198.5 38: (ns/day) (hour/ns) 38: Performance: 159.337 0.151 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (139 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.004 194.9 38: (ns/day) (hour/ns) 38: Performance: 333.456 0.072 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 69 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 197.9 38: (ns/day) (hour/ns) 38: Performance: 236.437 0.102 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (113 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 194.8 38: (ns/day) (hour/ns) 38: Performance: 347.252 0.069 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 72 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.007 197.9 38: (ns/day) (hour/ns) 38: Performance: 216.032 0.111 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (140 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 194.9 38: (ns/day) (hour/ns) 38: Performance: 337.844 0.071 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 62 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 197.2 38: (ns/day) (hour/ns) 38: Performance: 287.060 0.084 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (132 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.008 0.004 193.7 38: (ns/day) (hour/ns) 38: Performance: 344.263 0.070 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 66 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 197.7 38: (ns/day) (hour/ns) 38: Performance: 270.629 0.089 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (108 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.0 38: (ns/day) (hour/ns) 38: Performance: 317.409 0.076 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 78 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 198.4 38: (ns/day) (hour/ns) 38: Performance: 169.182 0.142 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (136 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.1 38: (ns/day) (hour/ns) 38: Performance: 309.718 0.077 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 69 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 198.0 38: (ns/day) (hour/ns) 38: Performance: 233.214 0.103 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (128 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.4 38: (ns/day) (hour/ns) 38: Performance: 297.340 0.081 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 66 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 197.8 38: (ns/day) (hour/ns) 38: Performance: 256.948 0.093 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (132 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 300.268 0.080 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 76 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.016 0.008 198.3 38: (ns/day) (hour/ns) 38: Performance: 180.938 0.133 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (108 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 314.943 0.076 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 68 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 197.6 38: (ns/day) (hour/ns) 38: Performance: 236.855 0.101 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (136 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 318.344 0.075 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 194.2 38: (ns/day) (hour/ns) 38: Performance: 641.795 0.037 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (110 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.0 38: (ns/day) (hour/ns) 38: Performance: 305.464 0.079 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 68 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 197.8 38: (ns/day) (hour/ns) 38: Performance: 242.124 0.099 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (126 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 317.229 0.076 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 194.7 38: (ns/day) (hour/ns) 38: Performance: 642.264 0.037 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (106 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 197.4 38: (ns/day) (hour/ns) 38: Performance: 162.386 0.148 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 194.6 38: (ns/day) (hour/ns) 38: Performance: 633.610 0.038 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (124 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.009 0.005 195.0 38: (ns/day) (hour/ns) 38: Performance: 315.750 0.076 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 63 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 197.5 38: (ns/day) (hour/ns) 38: Performance: 275.901 0.087 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (130 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 196.4 38: (ns/day) (hour/ns) 38: Performance: 208.501 0.115 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 77 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 198.4 38: (ns/day) (hour/ns) 38: Performance: 166.850 0.144 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (140 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 55 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.021 0.011 197.9 38: (ns/day) (hour/ns) 38: Performance: 135.249 0.177 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (single precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 76 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 198.2 38: (ns/day) (hour/ns) 38: Performance: 172.286 0.139 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.3 38: (ns/day) (hour/ns) 38: Performance: 288.363 0.083 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 70 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 197.9 38: (ns/day) (hour/ns) 38: Performance: 212.610 0.113 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (180 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.3 38: (ns/day) (hour/ns) 38: Performance: 293.571 0.082 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 70 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.007 197.9 38: (ns/day) (hour/ns) 38: Performance: 215.323 0.111 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (144 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 194.3 38: (ns/day) (hour/ns) 38: Performance: 293.978 0.082 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 198.0 38: (ns/day) (hour/ns) 38: Performance: 210.864 0.114 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (161 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.5 38: (ns/day) (hour/ns) 38: Performance: 293.950 0.082 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 71 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 198.0 38: (ns/day) (hour/ns) 38: Performance: 206.641 0.116 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (167 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 197.4 38: (ns/day) (hour/ns) 38: Performance: 159.324 0.151 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 77 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 198.3 38: (ns/day) (hour/ns) 38: Performance: 165.893 0.145 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (176 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 286.980 0.084 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 74 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 198.2 38: (ns/day) (hour/ns) 38: Performance: 191.507 0.125 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (176 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.1 38: (ns/day) (hour/ns) 38: Performance: 293.445 0.082 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 69 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 197.9 38: (ns/day) (hour/ns) 38: Performance: 202.791 0.118 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (176 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.2 38: (ns/day) (hour/ns) 38: Performance: 296.282 0.081 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 63 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 197.5 38: (ns/day) (hour/ns) 38: Performance: 270.605 0.089 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 46 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.018 0.009 197.4 38: (ns/day) (hour/ns) 38: Performance: 159.721 0.150 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 72 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 197.7 38: (ns/day) (hour/ns) 38: Performance: 205.957 0.117 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (168 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.3 38: (ns/day) (hour/ns) 38: Performance: 291.584 0.082 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 194.7 38: (ns/day) (hour/ns) 38: Performance: 607.134 0.040 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (153 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.019 0.010 197.0 38: (ns/day) (hour/ns) 38: Performance: 154.564 0.155 38: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (single precision) 38: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 194.9 38: (ns/day) (hour/ns) 38: Performance: 651.846 0.037 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as single precision energy file 38: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as single precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (156 ms) 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (4616 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 57 tests from 4 test cases ran. (9260 ms total) 38: [ PASSED ] 57 tests. 38/40 Test #38: MdrunNonIntegratorTests .......... Passed 9.32 sec test 39 Start 39: LegacyGroupSchemeMdrunTests 39: Test command: /build/gromacs-2019.1/build/basic/bin/legacy-mdrun-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml" 39: Test timeout computed to be: 600 39: [==========] Running 2 tests from 1 test case. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from Simple/TpiTest 39: [ RUN ] Simple/TpiTest.ReproducesOutput/0 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.1 (single precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 8.698e+02 8.698e+02 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (385 ms) 39: [ RUN ] Simple/TpiTest.ReproducesOutput/1 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.1 (single precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 9.151e+01 9.151e+01 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (397 ms) 39: [----------] 2 tests from Simple/TpiTest (782 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 2 tests from 1 test case ran. (782 ms total) 39: [ PASSED ] 2 tests. 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 0.80 sec test 40 Start 40: MdrunMpiTests 40: Test command: /build/gromacs-2019.1/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic/Testing/Temporary/MdrunMpiTests.xml" 40: Test timeout computed to be: 600 40: [==========] Running 21 tests from 7 test cases. 40: [----------] Global test environment set-up. 40: [----------] 1 test from DomainDecompositionSpecialCasesTest 40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1981966967 40: Generated 3 of the 3 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 3 of the 3 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 9.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc2' 40: 0 steps, 0.0 ps. 40: 40: NOTE: 93 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.010 0.005 196.8 40: (ns/day) (hour/ns) 40: Performance: 17.229 1.393 40: This run will generate roughly 0 Mb of data 40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (64 ms) 40: [----------] 1 test from DomainDecompositionSpecialCasesTest (64 ms total) 40: 40: [----------] 4 tests from MimicTest 40: [ RUN ] MimicTest.OneQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1067584090 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.008 0.004 198.1 40: (ns/day) (hour/ns) 40: Performance: 21.461 1.118 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.OneQuantumMol (98 ms) 40: [ RUN ] MimicTest.AllQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 793873733 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 91 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.011 0.006 198.6 40: (ns/day) (hour/ns) 40: Performance: 15.020 1.598 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.AllQuantumMol (51 ms) 40: [ RUN ] MimicTest.TwoQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -1011356392 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 93 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.013 0.007 199.0 40: (ns/day) (hour/ns) 40: Performance: 12.901 1.860 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.TwoQuantumMol (63 ms) 40: [ RUN ] MimicTest.BondCuts 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -677535691 40: Generated 2211 of the 2211 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2211 of the 2211 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 66.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: NVE simulation: will use the initial temperature of 300.368 K for 40: determining the Verlet buffer size 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 40: 40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 41 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 194.1 40: (ns/day) (hour/ns) 40: Performance: 81.619 0.294 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.BondCuts (49 ms) 40: [----------] 4 tests from MimicTest (261 ms total) 40: 40: [----------] 1 test from MultiSimTerminationTest 40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from MultiSimTerminationTest (0 ms total) 40: 40: [----------] 2 tests from PmeTest 40: [ RUN ] PmeTest.ReproducesEnergies 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: Setting the LD random seed to 1594253346 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 12.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: NVE simulation: will use the initial temperature of 1046.791 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108 40: This run will generate roughly 0 Mb of data 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.060 0.030 199.5 40: (ns/day) (hour/ns) 40: Performance: 60.291 0.398 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file 40: 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/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.060 0.030 199.5 40: (ns/day) (hour/ns) 40: Performance: 60.801 0.395 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file 40: 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/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.055 0.028 199.4 40: (ns/day) (hour/ns) 40: Performance: 65.361 0.367 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file 40: 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 ] PmeTest.ReproducesEnergies (10140 ms) 40: [ RUN ] PmeTest.ScalesTheBox 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -222061700 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Searching the wall atom type(s) 40: Number of degrees of freedom in T-Coupling group rest is 13.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: NVE simulation: will use the initial temperature of 966.268 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (single precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 0 steps, 0.0 ps. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.009 0.004 194.3 40: (ns/day) (hour/ns) 40: Performance: 19.212 1.249 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118 40: This run will generate roughly 0 Mb of data 40: [ OK ] PmeTest.ScalesTheBox (31983 ms) 40: [----------] 2 tests from PmeTest (42123 ms total) 40: 40: [----------] 1 test from ReplicaExchangeTerminationTest 40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 40: 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -4.7990940e+01 40: Maximum force = 1.8629752e+02 on atom 13 40: Norm of force = 8.7721851e+01 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (291 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 3.02331e+02 on atom 3 40: F-Norm = 1.18024e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -5.5862331e+01 40: Maximum force = 4.2726447e+02 on atom 13 40: Norm of force = 1.8452602e+02 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (289 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.1937726e+02 40: Maximum force = 9.9988691e+03 on atom 9 40: Norm of force = 4.6167015e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 40: 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 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (130 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: 40: NOTE 3 [file glycine_vacuo.top, line 12]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41575e+04 on atom 10 40: F-Norm = 1.18451e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.5174414e+02 40: Maximum force = 7.4208760e+03 on atom 9 40: Norm of force = 3.5692977e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 40: 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 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (128 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.5698456e+02 40: Maximum force = 4.5702225e+02 on atom 17 40: Norm of force = 1.8327095e+02 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 40: 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 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (19 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: 40: NOTE 4 [file unknown]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 5 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 5 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 1.06799e+03 on atom 28 40: F-Norm = 4.26914e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.6941235e+02 40: Maximum force = 2.1838159e+02 on atom 17 40: Norm of force = 7.9235189e+01 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 40: 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 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (20 ms) 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (877 ms total) 40: 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents converged to Fmax < 10 in 1 steps 40: Potential Energy = -9.7425687e-01 40: Maximum force = 4.0132279e+00 on atom 1 40: Norm of force = 1.6383933e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (8 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.9064195e-01 40: Maximum force = 2.5781672e+00 on atom 1 40: Norm of force = 1.0525324e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (14 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (single precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.9064195e-01 40: Maximum force = 2.5781672e+00 on atom 1 40: Norm of force = 1.0525324e+00 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (26 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.1939673e+02 40: Maximum force = 9.9704229e+03 on atom 9 40: Norm of force = 4.6227534e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (176 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (single precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.5625757e+02 40: Maximum force = 7.5018237e+03 on atom 9 40: Norm of force = 3.6139019e+03 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (180 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (single precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.8472457e+03 40: Maximum force = 2.1261648e+04 on atom 9 40: Norm of force = 1.0198873e+04 40: Opened /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (164 ms) 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (568 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 21 tests from 7 test cases ran. (43893 ms total) 40: [ PASSED ] 21 tests. 40: 40: YOU HAVE 4 DISABLED TESTS 40: 40/40 Test #40: MdrunMpiTests .................... Passed 43.92 sec 100% tests passed, 0 tests failed out of 40 Label Time Summary: GTest = 136.15 sec*proc (40 tests) IntegrationTest = 98.79 sec*proc (5 tests) MpiTest = 0.80 sec*proc (3 tests) SlowTest = 31.25 sec*proc (1 test) UnitTest = 6.11 sec*proc (34 tests) Total Test time (real) = 136.23 sec /usr/bin/make -j8 -C build/basic-dp tests make[1]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 84 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/external/googletest /build/gromacs-2019.1/build/basic-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build Scanning dependencies of target gmock [ 0%] Built target lmfit_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 0%] Built target mdrun_test_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc /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 cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= [ 1%] Built target mdrun_objlib /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 2%] Built target tng_io_obj make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 5%] Built target libgromacs_external Scanning dependencies of target analysisdata-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/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 Scanning dependencies of target mdrunutility-test-shared make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/datatest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/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 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/mock_datamodule.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp [ 19%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 79%] Built target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 79%] Built target mdrunutility-test-shared [ 79%] Built target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 79%] Built target analysisdata-test-shared cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 79%] 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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/testutils /build/gromacs-2019.1/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target testutils /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 /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/testutils/tests /build/gromacs-2019.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/testutils/tests /build/gromacs-2019.1/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-test Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build Scanning dependencies of target applied-forces-test Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/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]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Scanning dependencies of target domdec-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target mdrun-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Entering directory '/build/gromacs-2019.1/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 cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp /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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/domain_decomposition.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target testutils-mpi-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target listed-forces-test /usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/applied-forces-test.dir/electricfield.cpp.o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied-forces-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] Built target applied-forces-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 80%] 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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 82%] Built target fft-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisim.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 82%] Built target hardware-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/multisimtest.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.4.0.0 ../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 83%] Built target testutils-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 83%] Built target mdrunutility-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/replicaexchange.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] Built target gpu_utils-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] Built target mdrunutility-mpi-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] Built target mdrun-mpi-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 84%] 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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 85%] Built target mdlib-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 85%] 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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target commandline-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/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]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target taskassignment-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target utility-mpi-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] 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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target pull-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 86%] Built target table-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target random-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxana-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/entropy.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 88%] Built target compat-test /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/DependInfo.cmake --color= Scanning dependencies of target pdb2gmx-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_traj.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target math-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color= Scanning dependencies of target gmxpreprocess-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/genconf.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target fileio-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/insert-molecules.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/insert-molecules.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_trjconv.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/readir.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/pdb2gmx-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 89%] Built target pdb2gmx-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color= Scanning dependencies of target correlations-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/autocorr.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxana/tests/gmx_msd.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/solvate.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 90%] Built target awh-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color= Scanning dependencies of target analysisdata-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/analysisdata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxpreprocess-test.dir/genconf.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_trjconv.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 90%] Built target gmxpreprocess-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Scanning dependencies of target selection-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/indexutil.cpp [ 91%] Built target gmxana-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target trajectoryanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/moduletest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/correlationdataset.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /build/gromacs-2019.1/src/gromacs/correlationfunctions/tests/expfit.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 91%] Built target correlations-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color= Scanning dependencies of target energyanalysis-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/legacyenergy.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/nbsearch.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/angle.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 91%] Built target energyanalysis-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/arraydata.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/distance.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/average.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/pairdist.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target options-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color= Scanning dependencies of target tool-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/report-methods.cpp.o -c /build/gromacs-2019.1/src/gromacs/tools/tests/report-methods.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/rdf.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/poscalc.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/histogram.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/sasa.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/select.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /build/gromacs-2019.1/src/gromacs/analysisdata/tests/lifetime.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/tool-test.dir/report-methods.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target tool-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectioncollection.cpp Scanning dependencies of target mdrun-non-integrator-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/minimize.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/analysisdata-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target analysisdata-test /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target legacy-mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/legacy-mdrun-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tpitest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/rerun.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/legacy-mdrun-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/legacy-mdrun-test.dir/tpitest.cpp.o CMakeFiles/legacy-mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/legacy-mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 92%] Built target legacy-mdrun-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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun-test make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/compressed_x_output.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/trajectory.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/unionfind.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/grompp.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/grompp.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/initialconstraints.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-non-integrator-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 94%] Built target mdrun-non-integrator-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/interactiveMD.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/pmetest.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/swapcoords.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/selectionoption.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/termination.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/termination.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/trajectory_writing.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 96%] Built target simd-test cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/mimic.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/tests/mimic.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.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 ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o ../../analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -o ../../../../bin/trajectoryanalysis-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/tests/toputils.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp [ 98%] Built target trajectoryanalysis-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-test.dir/grompp.cpp.o CMakeFiles/mdrun-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/termination.cpp.o CMakeFiles/mdrun-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-test.dir/mimic.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrun_test_objlib.dir/energyreader.cpp.o CMakeFiles/mdrun_test_objlib.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/moduletest.cpp.o CMakeFiles/mdrun_test_objlib.dir/simulationdatabase.cpp.o CMakeFiles/mdrun_test_objlib.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_objlib.dir/trajectoryreader.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../../../bin/mdrun-test -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/basic-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target mdrun-test cd /build/gromacs-2019.1/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target selection-test cd /build/gromacs-2019.1/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/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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 -Wl,-rpath,/build/gromacs-2019.1/build/basic-dp/lib ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.4.0.0 ../../../../lib/libgmock.a -lpthread -fopenmp -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' (cd build/basic-dp; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/basic-dp/DartConfiguration.tcl Test project /build/gromacs-2019.1/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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/basic-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (5 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (11 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (0 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (1 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (2 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (20 ms total) 1: [ PASSED ] 59 tests. 1/40 Test #1: TestUtilsUnitTests ............... Passed 0.05 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /build/gromacs-2019.1/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (9 ms) 2: [----------] 1 test from MpiSelfTest (9 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (9 ms total) 2: [ PASSED ] 1 test. 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.03 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (5 ms) 3: [----------] 1 test from VerletBufferConstraintTest (5 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (1 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (1 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (2 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (10 ms total) 3: [ PASSED ] 50 tests. 3/40 Test #3: MdlibUnitTest .................... Passed 0.03 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/basic-dp/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (1 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 3 tests. 4/40 Test #4: AppliedForcesUnitTest ............ Passed 0.02 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/basic-dp/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (1 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (1 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (1 ms total) 5: [ PASSED ] 15 tests. 5/40 Test #5: ListedForcesTest ................. Passed 0.03 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/basic-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (5 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (7 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (18 ms total) 6: [ PASSED ] 55 tests. 6/40 Test #6: CommandLineUnitTests ............. Passed 0.04 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/basic-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (1 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (1 ms total) 7: [ PASSED ] 9 tests. 7/40 Test #7: DomDecTests ...................... Passed 0.02 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/basic-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (5 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (14 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (62 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (7 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (5 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (81 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (27 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (9 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (7 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (19 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (7 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (30 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (22 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (6 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (31 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (3 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (84 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (399 ms total) 8: [ PASSED ] 257 tests. 8/40 Test #8: EwaldUnitTests ................... Passed 0.47 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/basic-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (8 ms) 9: [----------] 2 tests from ManyFFTTest (16 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (2 ms) 9: [----------] 1 test from FFTTest (3 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (2 ms) 9: [----------] 1 test from FFFTest3D (3 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (5 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (8 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (20 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (42 ms total) 9: [ PASSED ] 14 tests. 9/40 Test #9: FFTUnitTests ..................... Passed 0.06 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (5 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (5 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (7 ms total) 10: [ PASSED ] 60 tests. 10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.03 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/basic-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (21 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (21 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (20 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (20 ms) 11: [----------] 4 tests from HardwareTopologyTest (82 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (82 ms total) 11: [ PASSED ] 4 tests. 11/40 Test #11: HardwareUnitTests ................ Passed 0.10 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/basic-dp/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (0 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (0 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (1 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (0 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (8 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (1 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (10 ms total) 12: [ PASSED ] 112 tests. 12/40 Test #12: MathUnitTests .................... Passed 0.03 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (5 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (5 ms total) 13: [ PASSED ] 17 tests. 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.03 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (73 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (72 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (43 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (35 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (64 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (48 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (337 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (40 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (44 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (48 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (47 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (52 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (59 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (44 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (336 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (674 ms total) 14: [ PASSED ] 13 tests. 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.69 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (1 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (1 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (4 ms total) 15: [ PASSED ] 22 tests. 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.02 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/basic-dp/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (1 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (1 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (0 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (1 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (1 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (1 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (9 ms total) 16: [ PASSED ] 110 tests. 16/40 Test #16: OptionsUnitTests ................. Passed 0.03 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/basic-dp/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (0 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (0 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (1 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (6 ms total) 17: [ PASSED ] 44 tests. 17/40 Test #17: RandomUnitTests .................. Passed 0.04 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/40 Test #18: RestraintTests ................... Passed 0.02 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/basic-dp/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (36 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (67 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (72 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (17 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (66 ms) 19: [----------] 10 tests from SplineTableTest/0 (269 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (2 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (85 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (5 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (171 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (179 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (40 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (162 ms) 19: [----------] 10 tests from SplineTableTest/1 (655 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (924 ms total) 19: [ PASSED ] 20 tests. 19/40 Test #19: TableUnitTests ................... Passed 0.95 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (1 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.02 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/basic-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (0 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (1 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (4 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (1 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (0 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (1 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (1 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (1 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (1 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 21: [----------] 7 tests from StringUtilityTest (0 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (1 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (1 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (1 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (20 ms total) 21: [ PASSED ] 325 tests. 21/40 Test #21: UtilityUnitTests ................. Passed 0.05 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /build/gromacs-2019.1/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (53 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (27 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (80 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (81 ms total) 22: [ PASSED ] 2 tests. 22/40 Test #22: UtilityMpiUnitTests .............. Passed 0.10 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/basic-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (1 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (5 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (5 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (3 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (1 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (6 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (12 ms total) 23: [ PASSED ] 17 tests. 23/40 Test #23: FileIOTests ...................... Passed 0.03 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/basic-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (0 ms total) 24: [ PASSED ] 5 tests. 24/40 Test #24: PullTest ......................... Passed 0.02 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/basic-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (2 ms) 25: [----------] 1 test from gridTest (2 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (0 ms) 25: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (0 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (0 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (9 ms total) 25: [ PASSED ] 12 tests. 25/40 Test #25: AwhTest .......................... Passed 0.03 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/basic-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 236 tests from 19 test cases. 26: [----------] Global test environment set-up. 26: [----------] 6 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [----------] 6 tests from SimdBootstrapTest (0 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 26: 26: [----------] 13 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [----------] 13 tests from SimdFloatingpointUtilTest (1 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (2 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (2 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (1 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (1 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (2 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (4 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (4 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (2 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (3 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (2 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (3 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (7 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (1 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (2 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (3 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (6 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (3 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (2 ms) 26: [----------] 45 tests from SimdMathTest (83 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (0 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 236 tests from 19 test cases ran. (85 ms total) 26: [ PASSED ] 236 tests. 26/40 Test #26: SimdUnitTests .................... Passed 0.11 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/basic-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/40 Test #27: CompatibilityHelpersTests ........ Passed 0.02 sec test 28 Start 28: GmxAnaTest 28: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GmxAnaTest.xml" 28: Test timeout computed to be: 600 28: [==========] Running 26 tests from 5 test cases. 28: [----------] Global test environment set-up. 28: [----------] 5 tests from Entropy 28: [ RUN ] Entropy.Schlitter_300_NoLinear 28: [ OK ] Entropy.Schlitter_300_NoLinear (0 ms) 28: [ RUN ] Entropy.Schlitter_300_Linear 28: [ OK ] Entropy.Schlitter_300_Linear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear 28: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms) 28: [ RUN ] Entropy.QuasiHarmonic_200_Linear 28: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms) 28: [----------] 5 tests from Entropy (1 ms total) 28: 28: [----------] 3 tests from MsdTest 28: [ RUN ] MsdTest.threeDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.threeDimensionalDiffusion (2 ms) 28: [ RUN ] MsdTest.twoDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.twoDimensionalDiffusion (1 ms) 28: [ RUN ] MsdTest.oneDimensionalDiffusion 28: 28: Select a group to calculate mean squared displacement for: 28: Group 0 ( particles) has 3 elements 28: There is one group in the index 28: 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 28: 28: Used 1 restart points spaced 200 ps over 9 ps 28: 28: Fitting from 1 to 8 ps 28: 28: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s 28: [ OK ] MsdTest.oneDimensionalDiffusion (2 ms) 28: [----------] 3 tests from MsdTest (5 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: trr version: GMX_trn_file (single precision) 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 28: Group 0 ( System) has 6 elements 28: Group 1 ( Water) has 6 elements 28: Group 2 ( SOL) has 6 elements 28: Select a group: Reading frame 0 time 0.000 Reading frame 1 time 0.000 Last frame 1 time 0.000 28: Selected 0: 'System' 28: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (8 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (21 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (4 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (4 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (3 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 28: Will write tng: Trajectory file (tng format) 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (3 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (19 ms total) 28: 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.tng is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (1 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (0 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from gro file '', 6 atoms. 28: Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.gro is 0.001 (nm) 28: -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (2 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frames from pdb file Reading frame 0 time 0.000 28: Precision of /build/gromacs-2019.1/src/gromacs/gmxana/tests/spc2-traj.pdb is 0.0001 (nm) 28: -> frame 0 time 0.000 't= 0.00000', 6 atoms 28: Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (0 ms) 28: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 28: Will write trr: Trajectory in portable xdr format 28: Group 0 ( System) has 6 elements 28: Group 1 (FirstWaterMolecule) has 3 elements 28: Group 2 (SecondWaterMolecule) has 3 elements 28: Select a group: Reading frame 0 time 0.000 -> frame 0 time 0.000 Reading frame 1 time 0.000 -> frame 1 time 0.000 Last frame 1 time 0.000 28: 28: Note that major changes are planned in future for trjconv, to improve usability and utility.Select group for output 28: Selected 2: 'SecondWaterMolecule' 28: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (0 ms) 28: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (7 ms total) 28: 28: [----------] Global test environment tear-down 28: [==========] 26 tests from 5 test cases ran. (53 ms total) 28: [ PASSED ] 26 tests. 28/40 Test #28: GmxAnaTest ....................... Passed 0.08 sec test 29 Start 29: GmxPreprocessTests 29: Test command: /build/gromacs-2019.1/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml" 29: Test timeout computed to be: 30 29: [==========] Running 26 tests from 4 test cases. 29: [----------] Global test environment set-up. 29: [----------] 4 tests from GenconfTest 29: [ RUN ] GenconfTest.nbox_Works 29: [ OK ] GenconfTest.nbox_Works (2 ms) 29: [ RUN ] GenconfTest.nbox_norenumber_Works 29: [ OK ] GenconfTest.nbox_norenumber_Works (0 ms) 29: [ RUN ] GenconfTest.nbox_dist_Works 29: [ OK ] GenconfTest.nbox_dist_Works (1 ms) 29: [ RUN ] GenconfTest.nbox_rot_Works 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: center of geometry: 1.733667, 1.477000, 0.905167 29: [ OK ] GenconfTest.nbox_rot_Works (1 ms) 29: [----------] 4 tests from GenconfTest (5 ms total) 29: 29: [----------] 5 tests from InsertMoleculesTest 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: 29: Added 1 molecules (out of 1 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro 29: 29: Output configuration contains 8 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (3 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: Try 3 success (now 6 atoms)! 29: Try 4 success (now 8 atoms)! 29: Try 5 success (now 10 atoms)! 29: 29: Added 5 molecules (out of 5 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro 29: 29: Output configuration contains 10 atoms in 10 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (3 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 8 atoms)! 29: Try 2 success (now 10 atoms)! 29: 29: Added 2 molecules (out of 2 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro 29: 29: Output configuration contains 10 atoms in 4 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (6 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 29: Reading solute configuration 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Try 1 success (now 650 atoms)! 29: Try 2 success (now 652 atoms)! 29: Try 3 success (now 654 atoms)! 29: Try 4 success (now 656 atoms)! 29: 29: Added 4 molecules (out of 4 requested) 29: Replaced 8 residues (24 atoms) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro 29: 29: Output configuration contains 632 atoms in 212 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (13 ms) 29: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Using random seed 1997 29: Read 4 positions from file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat 29: 29: Try 1 success (now 2 atoms)! 29: Try 2 success (now 4 atoms)! 29: 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) 29: Try 13 success (now 6 atoms)! 29: 29: Added 3 molecules (out of 4 requested) 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro 29: 29: Output configuration contains 6 atoms in 3 residues 29: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (3 ms) 29: [----------] 5 tests from InsertMoleculesTest (28 ms total) 29: 29: [----------] 12 tests from GetIrTest 29: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: Ignoring obsolete mdp entry 'title' 29: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' 29: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (4 ms) 29: [ RUN ] GetIrTest.HandlesOnlyCutoffScheme 29: [ OK ] GetIrTest.HandlesOnlyCutoffScheme (3 ms) 29: [ RUN ] GetIrTest.UserErrorsSilentlyTolerated 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.UserErrorsSilentlyTolerated (4 ms) 29: [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (8 ms) 29: [ RUN ] GetIrTest.EmptyInputWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.EmptyInputWorks (4 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricField 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricField (3 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (4 ms) 29: [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (4 ms) 29: [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys 29: [ OK ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys (7 ms) 29: [ RUN ] GetIrTest.ImplicitSolventNoWorks 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp, line 2]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ImplicitSolventNoWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.ImplicitSolventNoWorks (4 ms) 29: [ RUN ] GetIrTest.ImplicitSolventYesWorks 29: [ OK ] GetIrTest.ImplicitSolventYesWorks (6 ms) 29: [ RUN ] GetIrTest.HandlesMimic 29: 29: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp, line 3]: 29: /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesMimic_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 29: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 29: scheme was introduced, but the group scheme was still the default. The 29: default is now the Verlet scheme, so you will observe different behaviour. 29: 29: [ OK ] GetIrTest.HandlesMimic (4 ms) 29: [----------] 12 tests from GetIrTest (55 ms total) 29: 29: [----------] 5 tests from SolvateTest 29: [ RUN ] SolvateTest.cs_box_Works 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 1x1x1 boxes 29: Solvent box contains 270 atoms in 90 residues 29: Removed 129 solvent atoms due to solvent-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 47 residues 29: Generated solvent containing 141 atoms in 47 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro 29: 29: Output configuration contains 141 atoms in 47 residues 29: Volume : 1.331 (nm^3) 29: Density : 1056.36 (g/l) 29: Number of solvent molecules: 47 29: 29: [ OK ] SolvateTest.cs_box_Works (13 ms) 29: [ RUN ] SolvateTest.cs_cp_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.776 (g/l) 29: Number of solvent molecules: 886 29: 29: [ OK ] SolvateTest.cs_cp_Works (62 ms) 29: [ RUN ] SolvateTest.cs_cp_p_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 886 residues 29: Generated solvent containing 2658 atoms in 886 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro 29: 29: Output configuration contains 2664 atoms in 888 residues 29: Volume : 27.2709 (nm^3) 29: Density : 974.776 (g/l) 29: Number of solvent molecules: 886 29: 29: Processing topology 29: Adding line for 886 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works.top) 29: [ OK ] SolvateTest.cs_cp_p_Works (57 ms) 29: [ RUN ] SolvateTest.shell_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 2x2x2 boxes 29: Solvent box contains 3660 atoms in 1220 residues 29: Removed 987 solvent atoms due to solvent-solvent overlap 29: Removed 1902 solvent atoms more than 1.000000 nm from solute. 29: Removed 15 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 1 molecule type: 29: SOL ( 3 atoms): 252 residues 29: Generated solvent containing 756 atoms in 252 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro 29: 29: Output configuration contains 762 atoms in 254 residues 29: Volume : 27.2709 (nm^3) 29: Density : 279.3 (g/l) 29: Number of solvent molecules: 252 29: 29: [ OK ] SolvateTest.shell_Works (32 ms) 29: [ RUN ] SolvateTest.update_Topology_Works 29: Reading solute configuration 29: Reading solvent configuration 29: 29: Initialising inter-atomic distances... 29: 29: WARNING: Masses and atomic (Van der Waals) radii will be guessed 29: based on residue and atom names, since they could not be 29: definitively assigned from the information in your input 29: files. These guessed numbers might deviate from the mass 29: and radius of the atom type. Please check the output 29: files if necessary. 29: 29: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii 29: from the source below. This means the results may be different 29: compared to previous GROMACS versions. 29: 29: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 29: A. Bondi 29: van der Waals Volumes and Radii 29: J. Phys. Chem. 68 (1964) pp. 441-451 29: -------- -------- --- Thank You --- -------- -------- 29: 29: Generating solvent configuration 29: Will generate new solvent configuration of 3x3x3 boxes 29: Solvent box contains 14952 atoms in 4984 residues 29: Removed 2787 solvent atoms due to solvent-solvent overlap 29: Removed 30 solvent atoms due to solute-solvent overlap 29: Sorting configuration 29: Found 2 different molecule types: 29: HOH ( 3 atoms): 1876 residues 29: SOL ( 3 atoms): 2169 residues 29: Generated solvent containing 0 atoms in 0 residues 29: Writing generated configuration to /build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro 29: 29: Output configuration contains 12141 atoms in 4047 residues 29: Volume : 125 (nm^3) 29: Density : 968.963 (g/l) 29: Number of solvent molecules: 4045 29: 29: Processing topology 29: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/build/gromacs-2019.1/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top) 29: [ OK ] SolvateTest.update_Topology_Works (226 ms) 29: [----------] 5 tests from SolvateTest (390 ms total) 29: 29: [----------] Global test environment tear-down 29: [==========] 26 tests from 4 test cases ran. (478 ms total) 29: [ PASSED ] 26 tests. 29/40 Test #29: GmxPreprocessTests ............... Passed 0.50 sec test 30 Start 30: Pdb2gmxTest 30: Test command: /build/gromacs-2019.1/build/basic-dp/bin/pdb2gmx-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/Pdb2gmxTest.xml" 30: Test timeout computed to be: 480 30: [==========] Running 80 tests from 6 test cases. 30: [----------] Global test environment set-up. 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (459 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (521 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (477 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (440 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (504 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (603 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (553 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (486 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (483 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (517 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (476 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (425 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (499 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (560 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (525 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip4p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (466 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (474 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (533 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (486 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (441 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 663 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.112 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (505 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 778 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.357 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (575 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 696 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.128 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (533 ms) 30: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 Atomtype 214 Atomtype 215 Atomtype 216 Atomtype 217 Atomtype 218 Atomtype 219 Atomtype 220 Atomtype 221 Atomtype 222 Atomtype 223 Atomtype 224 Atomtype 225 Atomtype 226 Atomtype 227 Atomtype 228 Atomtype 229 Atomtype 230 Atomtype 231 Atomtype 232 Atomtype 233 Atomtype 234 Atomtype 235 Atomtype 236 Atomtype 237 Atomtype 238 Atomtype 239 Atomtype 240 Atomtype 241 Atomtype 242 Atomtype 243 Atomtype 244 Atomtype 245 Atomtype 246 Atomtype 247 Atomtype 248 Atomtype 249 Atomtype 250 Atomtype 251 Atomtype 252 Atomtype 253 Atomtype 254 Atomtype 255 Atomtype 256 Atomtype 257 Atomtype 258 Atomtype 259 Atomtype 260 Atomtype 261 Atomtype 262 Atomtype 263 Atomtype 264 Atomtype 265 Atomtype 266 Atomtype 267 Atomtype 268 Atomtype 269 Atomtype 270 Atomtype 271 Atomtype 272 Atomtype 273 Atomtype 274 Atomtype 275 Atomtype 276 Atomtype 277 Atomtype 278 Atomtype 279 Atomtype 280 Atomtype 281 Atomtype 282 Atomtype 283 Atomtype 284 Atomtype 285 Atomtype 286 Atomtype 287 Atomtype 288 Atomtype 289 Atomtype 290 Atomtype 291 Atomtype 292 Atomtype 293 Atomtype 294 Atomtype 295 Atomtype 296 Atomtype 297 Atomtype 298 Atomtype 299 Atomtype 300 Atomtype 301 Atomtype 302 Atomtype 303 Atomtype 304 Atomtype 305 Atomtype 306 Atomtype 307 Atomtype 308 Atomtype 309 Atomtype 310 Atomtype 311 Atomtype 312 Atomtype 313 Atomtype 314 Atomtype 315 Atomtype 316 Atomtype 317 Atomtype 318 Atomtype 319 Atomtype 320 Atomtype 321 Atomtype 322 Atomtype 323 Atomtype 324 Atomtype 325 Atomtype 326 Atomtype 327 Atomtype 328 Atomtype 329 Atomtype 330 Atomtype 331 Atomtype 332 Atomtype 333 Atomtype 334 Atomtype 335 Atomtype 336 Atomtype 337 Atomtype 338 Atomtype 339 Atomtype 340 Atomtype 341 Atomtype 342 Atomtype 343 Atomtype 344 Atomtype 345 Atomtype 346 Atomtype 347 Atomtype 348 Atomtype 349 Atomtype 350 Atomtype 351 Atomtype 352 Atomtype 353 Atomtype 354 Atomtype 355 Atomtype 356 Atomtype 357 Atomtype 358 Atomtype 359 Atomtype 360 Atomtype 361 Atomtype 362 Atomtype 363 Atomtype 364 Atomtype 365 Atomtype 366 Atomtype 367 Atomtype 368 Atomtype 369 Atomtype 370 Atomtype 371 Atomtype 372 Atomtype 373 Atomtype 374 Atomtype 375 Atomtype 376 Atomtype 377 Atomtype 378 Atomtype 379 Atomtype 380 Atomtype 381 Atomtype 382 Atomtype 383 Atomtype 384 Atomtype 385 Atomtype 386 Atomtype 387 Atomtype 388 Atomtype 389 Atomtype 390 Atomtype 391 Atomtype 392 Atomtype 393 Atomtype 394 Atomtype 395 Atomtype 396 Atomtype 397 Atomtype 398 Atomtype 399 Atomtype 400 Atomtype 401 Atomtype 402 Atomtype 403 Atomtype 404 Atomtype 405 Atomtype 406 Atomtype 407 Atomtype 408 Atomtype 409 Atomtype 410 Atomtype 411 Atomtype 412 Atomtype 413 Atomtype 414 Atomtype 415 Atomtype 416 Atomtype 417 Atomtype 418 Atomtype 419 Atomtype 420 Atomtype 421 Atomtype 422 Atomtype 423 Atomtype 424 Atomtype 425 Atomtype 426 Atomtype 427 Atomtype 428 Atomtype 429 Atomtype 430 Atomtype 431 Atomtype 432 Atomtype 433 Atomtype 434 Atomtype 435 Atomtype 436 Atomtype 437 Atomtype 438 Atomtype 439 Atomtype 440 Atomtype 441 Atomtype 442 Atomtype 443 Atomtype 444 Atomtype 445 Atomtype 446 Atomtype 447 Atomtype 448 Atomtype 449 Atomtype 450 Atomtype 451 Atomtype 452 Atomtype 453 Atomtype 454 Atomtype 455 Atomtype 456 Atomtype 457 Atomtype 458 Atomtype 459 Atomtype 460 Atomtype 461 Atomtype 462 Atomtype 463 Atomtype 464 Atomtype 465 Atomtype 466 Atomtype 467 Atomtype 468 Atomtype 469 Atomtype 470 Atomtype 471 Atomtype 472 Atomtype 473 Atomtype 474 Atomtype 475 Atomtype 476 Atomtype 477 Atomtype 478 Atomtype 479 Atomtype 480 Atomtype 481 Atomtype 482 Atomtype 483 Atomtype 484 Atomtype 485 Atomtype 486 Atomtype 487 Atomtype 488 Atomtype 489 Atomtype 490 Atomtype 491 Atomtype 492 Atomtype 493 Atomtype 494 Atomtype 495 Atomtype 496 Atomtype 497 Atomtype 498 Atomtype 499 Atomtype 500 Atomtype 501 Atomtype 502 Atomtype 503 Atomtype 504 Atomtype 505 Atomtype 506 Atomtype 507 Atomtype 508 Atomtype 509 Atomtype 510 Atomtype 511 Atomtype 512 Atomtype 513 Atomtype 514 Atomtype 515 Atomtype 516 Atomtype 517 Atomtype 518 Atomtype 519 Atomtype 520 Atomtype 521 Atomtype 522 Atomtype 523 Atomtype 524 Atomtype 525 Atomtype 526 Atomtype 527 Atomtype 528 Atomtype 529 Atomtype 530 Atomtype 531 Atomtype 532 Atomtype 533 Atomtype 534 Atomtype 535 Atomtype 536 Atomtype 537 Atomtype 538 Atomtype 539 Atomtype 540 Atomtype 541 Atomtype 542 Atomtype 543 Atomtype 544 Atomtype 545 Atomtype 546 Atomtype 547 Atomtype 548 Atomtype 549 Atomtype 550 Atomtype 551 Atomtype 552 Atomtype 553 Atomtype 554 Atomtype 555 Atomtype 556 Atomtype 557 Atomtype 558 Atomtype 559 Atomtype 560 Atomtype 561 Atomtype 562 Atomtype 563 Atomtype 564 Atomtype 565 Atomtype 566 Atomtype 567 Atomtype 568 Atomtype 569 Atomtype 570 Atomtype 571 Atomtype 572 Atomtype 573 Atomtype 574 Atomtype 575 Atomtype 576 Atomtype 577 Atomtype 578 Atomtype 579 Atomtype 580 Atomtype 581 Atomtype 582 Atomtype 583 Atomtype 584 Atomtype 585 Atomtype 586 Atomtype 587 Atomtype 588 Atomtype 589 Atomtype 590 Atomtype 591 Atomtype 592 Atomtype 593 Atomtype 594 Atomtype 595 Atomtype 596 Atomtype 597 Atomtype 598 Atomtype 599 Atomtype 600 Atomtype 601 Atomtype 602 Atomtype 603 Atomtype 604 Atomtype 605 Atomtype 606 Atomtype 607 Atomtype 608 Atomtype 609 Atomtype 610 Atomtype 611 Atomtype 612 Atomtype 613 Atomtype 614 Atomtype 615 Atomtype 616 Atomtype 617 Atomtype 618 Atomtype 619 Atomtype 620 Atomtype 621 Atomtype 622 Atomtype 623 Atomtype 624 Atomtype 625 Atomtype 626 Atomtype 627 Atomtype 628 Atomtype 629 Atomtype 630 Atomtype 631 Atomtype 632 Atomtype 633 Atomtype 634 Atomtype 635 Atomtype 636 Atomtype 637 Atomtype 638 Atomtype 639 Atomtype 640 Atomtype 641 Atomtype 642 Atomtype 643 Atomtype 644 Atomtype 645 Atomtype 646 Atomtype 647 Atomtype 648 Atomtype 649 Atomtype 650 Atomtype 651 Atomtype 652 Atomtype 653 Atomtype 654 Atomtype 655 Atomtype 656 Atomtype 657 Atomtype 658 Atomtype 659 Atomtype 660 Atomtype 661 Atomtype 662 Atomtype 663 Atomtype 664 Atomtype 665 Atomtype 666 Atomtype 667 Atomtype 668 Atomtype 669 Atomtype 670 Atomtype 671 Atomtype 672 Atomtype 673 Atomtype 674 Atomtype 675 Atomtype 676 Atomtype 677 Atomtype 678 Atomtype 679 Atomtype 680 Atomtype 681 Atomtype 682 Atomtype 683 Atomtype 684 Atomtype 685 Atomtype 686 Atomtype 687 Atomtype 688 Atomtype 689 Atomtype 690 Atomtype 691 Atomtype 692 Atomtype 693 Atomtype 694 Atomtype 695 Atomtype 696 Atomtype 697 Atomtype 698 Atomtype 699 Atomtype 700 Atomtype 701 Atomtype 702 Atomtype 703 Atomtype 704 Atomtype 705 Atomtype 706 Atomtype 707 Atomtype 708 Atomtype 709 Atomtype 710 Atomtype 711 Atomtype 712 Atomtype 713 Atomtype 714 Atomtype 715 Atomtype 716 Atomtype 717 Atomtype 718 Atomtype 719 Atomtype 720 Atomtype 721 Atomtype 722 Atomtype 723 Atomtype 724 Atomtype 725 Atomtype 726 Atomtype 727 Atomtype 728 Atomtype 729 Atomtype 730 Atomtype 731 Atomtype 732 Atomtype 733 Atomtype 734 Atomtype 735 Atomtype 736 Atomtype 737 Atomtype 738 Atomtype 739 Atomtype 740 Atomtype 741 Atomtype 742 Atomtype 743 Atomtype 744 Atomtype 745 Atomtype 746 Atomtype 747 Atomtype 748 Atomtype 749 Atomtype 750 Atomtype 751 Atomtype 752 Atomtype 753 Atomtype 754 Atomtype 755 Atomtype 756 Atomtype 757 Atomtype 758 Atomtype 759 Atomtype 760 Atomtype 761 Atomtype 762 Atomtype 763 Atomtype 764 Atomtype 765 Atomtype 766 Atomtype 767 Atomtype 768 Atomtype 769 Atomtype 770 Atomtype 771 Atomtype 772 Atomtype 773 Atomtype 774 Atomtype 775 Atomtype 776 Atomtype 777 Atomtype 778 Atomtype 779 Atomtype 780 Atomtype 781 Atomtype 782 Atomtype 783 Atomtype 784 Atomtype 785 Atomtype 786 Atomtype 787 Atomtype 788 Atomtype 789 Atomtype 790 Atomtype 791 Atomtype 792 Atomtype 793 Atomtype 794 Atomtype 795 Atomtype 796 Atomtype 797 Atomtype 798 Atomtype 799 Atomtype 800 Atomtype 801 Atomtype 802 Atomtype 803 Atomtype 804 Atomtype 805 Atomtype 806 Atomtype 807 Atomtype 808 Atomtype 809 Atomtype 810 Atomtype 811 Atomtype 812 Atomtype 813 Atomtype 814 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/oplsaa.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 618 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.883 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Oplsaa force field in directory oplsaa.ff 30: 30: going to rename oplsaa.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Oplsaa) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: PRO-COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Oplsaa force field and the tip5p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (467 ms) 30: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (12012 ms total) 30: 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (248 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (284 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (253 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (234 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (258 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (307 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (262 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (243 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (235 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (280 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (250 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (229 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 172, now 167 30: Marked 37 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 305 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 77 impropers, 241 angles 30: 267 pairs, 167 bonds and 37 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 165 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (257 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 216, now 211 30: Marked 53 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 429 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 134 impropers, 316 angles 30: 273 pairs, 211 bonds and 51 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 202 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (299 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 179, now 174 30: Marked 36 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 349 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 102 impropers, 260 angles 30: 242 pairs, 174 bonds and 36 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 168 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (256 ms) 30: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos43a1.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 159, now 154 30: Marked 33 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 299 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 80 impropers, 227 angles 30: 232 pairs, 154 bonds and 31 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos43a1 force field in directory gromos43a1.ff 30: 30: going to rename gromos43a1.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos43a1) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 150 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos43a1 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (232 ms) 30: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (4129 ms total) 30: 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (250 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (292 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (251 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (233 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (263 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (309 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (270 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spc water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (247 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 0 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (249 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (298 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 0 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (254 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 0 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (233 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Making bonds... 30: Number of bonds was 174, now 169 30: Marked 39 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 267 pairs 30: Before cleaning: 312 dihedrals 30: Making cmap torsions... 30: There are 90 dihedrals, 79 impropers, 245 angles 30: 267 pairs, 169 bonds and 39 virtual sites 30: Total mass 1846.116 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 167 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (262 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Making bonds... 30: Number of bonds was 220, now 215 30: Marked 57 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 273 pairs 30: Before cleaning: 443 dihedrals 30: Making cmap torsions... 30: There are 93 dihedrals, 138 impropers, 324 angles 30: 273 pairs, 215 bonds and 55 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 206 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (311 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Making bonds... 30: Number of bonds was 181, now 176 30: Marked 38 virtual sites 30: Added 4 dummy masses 30: Added 8 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 242 pairs 30: Before cleaning: 356 dihedrals 30: Making cmap torsions... 30: There are 81 dihedrals, 104 impropers, 264 angles 30: 242 pairs, 176 bonds and 38 virtual sites 30: Total mass 1861.132 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 170 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (267 ms) 30: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.rtp 30: Using default: not generating all possible dihedrals 30: Using default: excluding 3 bonded neighbors 30: Using default: generating 1,4 H--H interactions 30: Using default: removing proper dihedrals found on the same bond as a proper dihedral 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/gromos53a6.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Making bonds... 30: Number of bonds was 161, now 156 30: Marked 35 virtual sites 30: Added 4 dummy masses 30: Added 10 new constraints 30: Generating angles, dihedrals and pairs... 30: 30: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom H used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: 30: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped 30: to an entry in the topology database, but the atom O used in 30: an interaction of type angle in that entry is not found in the 30: input file. Perhaps your atom and/or residue naming needs to be 30: fixed. 30: 30: 30: Before cleaning: 232 pairs 30: Before cleaning: 306 dihedrals 30: Making cmap torsions... 30: There are 78 dihedrals, 82 impropers, 231 angles 30: 232 pairs, 156 bonds and 33 virtual sites 30: Total mass 1662.887 a.m.u. 30: Total charge -0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Gromos53a6 force field in directory gromos53a6.ff 30: 30: going to rename gromos53a6.ff/aminoacids.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Gromos53a6) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 152 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Gromos53a6 force field and the spce water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (244 ms) 30: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (4235 ms total) 30: 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (456 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (518 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (484 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (432 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 255, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 691 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 691 dihedrals, 51 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.132 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (505 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 291, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 788 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 788 dihedrals, 72 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.366 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (562 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 262, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 727 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 727 dihedrals, 56 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.124 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (522 ms) 30: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 Residue 45 Residue 46 Residue 47 Residue 48 Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 Residue 61 Residue 62 Residue 63 Residue 64 Residue 65 Residue 66 Residue 67 Residue 68 Residue 69 Residue 70 Residue 71 Residue 72 Residue 73 Residue 74 Residue 75 Residue 76 Residue 77 Residue 78 Residue 79 Residue 80 Residue 81 Residue 82 Residue 83 Residue 84 Residue 85 Residue 86 Residue 87 Residue 88 Residue 89 Residue 90 Residue 91 Residue 92 Residue 93 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.rtp 30: Residue 94 Residue 95 Residue 96 Residue 97 Residue 98 Residue 99 Residue 100 Residue 101 Residue 102 Residue 103 Residue 104 Residue 105 Residue 106 Residue 107 Residue 108 Residue 109 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.rtp 30: Residue 110 Residue 111 Residue 112 Residue 113 Residue 114 Residue 115 Residue 116 Residue 117 Residue 118 Residue 119 Residue 120 Residue 121 Residue 122 Residue 123 Residue 124 Residue 125 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/amber99sb-ildn.ff/rna.arn 30: Making bonds... 30: Number of bonds was 233, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 634 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 634 dihedrals, 48 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.888 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff 30: 30: going to rename amber99sb-ildn.ff/aminoacids.r2b 30: going to rename amber99sb-ildn.ff/dna.r2b 30: going to rename amber99sb-ildn.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Amber99sb-ildn) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Amber99sb-ildn force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (487 ms) 30: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (3967 ms total) 30: 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 0 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (514 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 0 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (573 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 0 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (521 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 0 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (464 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 254, now 254 30: Marked 124 virtual sites 30: Added 16 dummy masses 30: Added 26 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 653 pairs 30: Before cleaning: 663 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 663 dihedrals, 48 impropers, 457 angles 30: 650 pairs, 254 bonds and 130 virtual sites 30: Total mass 1846.115 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 128 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (128 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 252 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment1.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (555 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 30 donors and 22 acceptors were found. 30: There are 36 hydrogen bonds 30: Will use HISE for residue 29 30: Will use HISE for residue 32 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS27 HIS29 30: SG90 NE2111 30: HIS29 NE2111 0.987 30: HIS32 NE2135 1.590 1.155 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 290, now 290 30: Marked 132 virtual sites 30: Added 10 dummy masses 30: Added 19 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 748 pairs 30: Before cleaning: 778 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 778 dihedrals, 49 impropers, 516 angles 30: 736 pairs, 290 bonds and 133 virtual sites 30: Total mass 2088.361 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb... 30: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 149 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (149 atoms, 16 residues) 30: Identified residue THR18 as a starting terminus. 30: Identified residue PHE33 as a ending terminus. 30: Start terminus THR-18: NH3+ 30: End terminus PHE-33: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 281 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment2.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (607 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 22 acceptors were found. 30: There are 26 hydrogen bonds 30: Will use HISE for residue 45 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS45 30: NE295 30: MET46 SD102 1.078 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 261, now 261 30: Marked 123 virtual sites 30: Added 22 dummy masses 30: Added 35 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 676 pairs 30: Before cleaning: 696 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 696 dihedrals, 39 impropers, 472 angles 30: 667 pairs, 261 bonds and 132 virtual sites 30: Total mass 1861.130 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb... 30: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 132 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (132 atoms, 16 residues) 30: Identified residue ALA34 as a starting terminus. 30: Identified residue ALA49 as a ending terminus. 30: Start terminus ALA-34: NH3+ 30: End terminus ALA-49: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment3.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (562 ms) 30: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 22 donors and 21 acceptors were found. 30: There are 30 hydrogen bonds 30: Will use HISE for residue 60 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS60 30: NE285 30: CYS62 SG98 0.803 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 232, now 232 30: Marked 111 virtual sites 30: Added 18 dummy masses 30: Added 31 new constraints 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 603 pairs 30: Before cleaning: 618 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 14 cmap torsion pairs 30: There are 618 dihedrals, 38 impropers, 419 angles 30: 597 pairs, 232 bonds and 116 virtual sites 30: Total mass 1662.885 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb... 30: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms 30: 30: chain #res #atoms 30: 1 ' ' 16 117 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 (117 atoms, 16 residues) 30: Identified residue LYS50 as a starting terminus. 30: Identified residue PRO65 as a ending terminus. 30: Start terminus LYS-50: NH3+ 30: End terminus PRO-65: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 228 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/fragment4.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (508 ms) 30: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (4304 ms total) 30: 30: [----------] 8 tests from ChainSep/Pdb2gmxTest 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (494 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 7 acceptors were found. 30: There are 7 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: HIS8 30: NE223 30: MET12 SD55 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 125, now 125 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 317 pairs 30: Before cleaning: 322 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 5 cmap torsion pairs 30: There are 322 dihedrals, 19 impropers, 227 angles 30: 314 pairs, 125 bonds and 0 virtual sites 30: Total mass 846.083 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on changing chain id only (ignoring TER records). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 7 58 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (58 atoms, 7 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 7 residues with 124 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 124 atoms 7 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (87 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 258, now 258 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 651 pairs 30: Before cleaning: 661 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 10 cmap torsion pairs 30: There are 661 dihedrals, 46 impropers, 463 angles 30: 648 pairs, 258 bonds and 0 virtual sites 30: Total mass 1882.146 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: 30: Merged chains into joint molecule definitions at 2 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 258 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (495 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 10 donors and 12 acceptors were found. 30: There are 13 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 30: SG9 30: HIS8 NE251 1.055 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 115, now 115 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 288 pairs 30: Before cleaning: 293 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 6 cmap torsion pairs 30: There are 293 dihedrals, 23 impropers, 203 angles 30: 285 pairs, 115 bonds and 0 virtual sites 30: Total mass 888.952 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 258 atoms and 16 residues 30: Total mass in system 1882.146 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records only (ignoring chain id). 30: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 8 61 30: 2 'B' 3 25 30: 3 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (61 atoms, 8 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 8 residues with 114 atoms 30: Chain time... 30: Processing chain 2 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 3 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 114 atoms 8 residues 30: Including chain 2 in system: 61 atoms 3 residues 30: Including chain 3 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (83 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 260, now 260 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 650 pairs 30: Before cleaning: 660 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 8 cmap torsion pairs 30: There are 660 dihedrals, 45 impropers, 466 angles 30: 647 pairs, 260 bonds and 0 virtual sites 30: Total mass 1900.162 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: 30: Merged chains into joint molecule definitions at 3 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 261 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (491 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 50, now 50 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 123 pairs 30: Before cleaning: 123 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 123 dihedrals, 9 impropers, 88 angles 30: 123 pairs, 50 bonds and 0 virtual sites 30: Total mass 434.421 a.m.u. 30: Total charge -2.000 e 30: Writing topology 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 6 donors and 4 acceptors were found. 30: There are 3 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 67, now 67 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 164 pairs 30: Before cleaning: 169 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 2 cmap torsion pairs 30: There are 169 dihedrals, 13 impropers, 118 angles 30: 161 pairs, 67 bonds and 0 virtual sites 30: Total mass 472.547 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 60, now 60 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 152 pairs 30: Before cleaning: 152 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 1 cmap torsion pairs 30: There are 152 dihedrals, 5 impropers, 112 angles 30: 152 pairs, 60 bonds and 0 virtual sites 30: Total mass 391.552 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 261 atoms and 16 residues 30: Total mass in system 1900.162 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records or chain id changing. 30: WARNING: Chain identifier 'B' is used in two non-sequential blocks. 30: They will be treated as separate chains unless you reorder your file. 30: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 4 28 30: 2 'B' 4 33 30: 3 'B' 3 25 30: 4 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (28 atoms, 4 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue GLU5 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus GLU-5: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 51 atoms 30: Chain time... 30: Processing chain 2 'B' (33 atoms, 4 residues) 30: Identified residue PHE6 as a starting terminus. 30: Identified residue ILE9 as a ending terminus. 30: Start terminus PHE-6: NH3+ 30: End terminus ILE-9: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 4 residues with 66 atoms 30: Chain time... 30: Processing chain 3 'B' (25 atoms, 3 residues) 30: Identified residue LYS10 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus LYS-10: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 3 residues with 61 atoms 30: Chain time... 30: Processing chain 4 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 51 atoms 4 residues 30: Including chain 2 in system: 66 atoms 4 residues 30: Including chain 3 in system: 61 atoms 3 residues 30: Including chain 4 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (85 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 25 donors and 23 acceptors were found. 30: There are 41 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 256, now 256 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 652 pairs 30: Before cleaning: 662 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 12 cmap torsion pairs 30: There are 662 dihedrals, 47 impropers, 460 angles 30: 649 pairs, 256 bonds and 0 virtual sites 30: Total mass 1864.131 a.m.u. 30: Total charge 0.000 e 30: Writing topology 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: 30: Merged chains into joint molecule definitions at 1 places. 30: 30: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 16 127 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (127 atoms, 16 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 16 residues with 255 atoms 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (503 ms) 30: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.r2b 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.r2b 30: All occupancies are one 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/atomtypes.atp 30: Atomtype 1 Atomtype 2 Atomtype 3 Atomtype 4 Atomtype 5 Atomtype 6 Atomtype 7 Atomtype 8 Atomtype 9 Atomtype 10 Atomtype 11 Atomtype 12 Atomtype 13 Atomtype 14 Atomtype 15 Atomtype 16 Atomtype 17 Atomtype 18 Atomtype 19 Atomtype 20 Atomtype 21 Atomtype 22 Atomtype 23 Atomtype 24 Atomtype 25 Atomtype 26 Atomtype 27 Atomtype 28 Atomtype 29 Atomtype 30 Atomtype 31 Atomtype 32 Atomtype 33 Atomtype 34 Atomtype 35 Atomtype 36 Atomtype 37 Atomtype 38 Atomtype 39 Atomtype 40 Atomtype 41 Atomtype 42 Atomtype 43 Atomtype 44 Atomtype 45 Atomtype 46 Atomtype 47 Atomtype 48 Atomtype 49 Atomtype 50 Atomtype 51 Atomtype 52 Atomtype 53 Atomtype 54 Atomtype 55 Atomtype 56 Atomtype 57 Atomtype 58 Atomtype 59 Atomtype 60 Atomtype 61 Atomtype 62 Atomtype 63 Atomtype 64 Atomtype 65 Atomtype 66 Atomtype 67 Atomtype 68 Atomtype 69 Atomtype 70 Atomtype 71 Atomtype 72 Atomtype 73 Atomtype 74 Atomtype 75 Atomtype 76 Atomtype 77 Atomtype 78 Atomtype 79 Atomtype 80 Atomtype 81 Atomtype 82 Atomtype 83 Atomtype 84 Atomtype 85 Atomtype 86 Atomtype 87 Atomtype 88 Atomtype 89 Atomtype 90 Atomtype 91 Atomtype 92 Atomtype 93 Atomtype 94 Atomtype 95 Atomtype 96 Atomtype 97 Atomtype 98 Atomtype 99 Atomtype 100 Atomtype 101 Atomtype 102 Atomtype 103 Atomtype 104 Atomtype 105 Atomtype 106 Atomtype 107 Atomtype 108 Atomtype 109 Atomtype 110 Atomtype 111 Atomtype 112 Atomtype 113 Atomtype 114 Atomtype 115 Atomtype 116 Atomtype 117 Atomtype 118 Atomtype 119 Atomtype 120 Atomtype 121 Atomtype 122 Atomtype 123 Atomtype 124 Atomtype 125 Atomtype 126 Atomtype 127 Atomtype 128 Atomtype 129 Atomtype 130 Atomtype 131 Atomtype 132 Atomtype 133 Atomtype 134 Atomtype 135 Atomtype 136 Atomtype 137 Atomtype 138 Atomtype 139 Atomtype 140 Atomtype 141 Atomtype 142 Atomtype 143 Atomtype 144 Atomtype 145 Atomtype 146 Atomtype 147 Atomtype 148 Atomtype 149 Atomtype 150 Atomtype 151 Atomtype 152 Atomtype 153 Atomtype 154 Atomtype 155 Atomtype 156 Atomtype 157 Atomtype 158 Atomtype 159 Atomtype 160 Atomtype 161 Atomtype 162 Atomtype 163 Atomtype 164 Atomtype 165 Atomtype 166 Atomtype 167 Atomtype 168 Atomtype 169 Atomtype 170 Atomtype 171 Atomtype 172 Atomtype 173 Atomtype 174 Atomtype 175 Atomtype 176 Atomtype 177 Atomtype 178 Atomtype 179 Atomtype 180 Atomtype 181 Atomtype 182 Atomtype 183 Atomtype 184 Atomtype 185 Atomtype 186 Atomtype 187 Atomtype 188 Atomtype 189 Atomtype 190 Atomtype 191 Atomtype 192 Atomtype 193 Atomtype 194 Atomtype 195 Atomtype 196 Atomtype 197 Atomtype 198 Atomtype 199 Atomtype 200 Atomtype 201 Atomtype 202 Atomtype 203 Atomtype 204 Atomtype 205 Atomtype 206 Atomtype 207 Atomtype 208 Atomtype 209 Atomtype 210 Atomtype 211 Atomtype 212 Atomtype 213 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.rtp 30: Residue 1 Residue 2 Residue 3 Residue 4 Residue 5 Residue 6 Residue 7 Residue 8 Residue 9 Residue 10 Residue 11 Residue 12 Residue 13 Residue 14 Residue 15 Residue 16 Residue 17 Residue 18 Residue 19 Residue 20 Residue 21 Residue 22 Residue 23 Residue 24 Residue 25 Residue 26 Residue 27 Residue 28 Residue 29 Residue 30 Residue 31 Residue 32 Residue 33 Residue 34 Residue 35 Residue 36 Residue 37 Residue 38 Residue 39 Residue 40 Residue 41 Residue 42 Residue 43 Residue 44 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.rtp 30: Residue 45 Residue 46 Residue 47 Residue 48 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.rtp 30: Residue 49 Residue 50 Residue 51 Residue 52 Residue 53 Residue 54 Residue 55 Residue 56 Residue 57 Residue 58 Residue 59 Residue 60 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.rtp 30: Residue 61 Residue 62 Residue 63 Residue 64 30: Sorting it all out... 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/lipids.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.hdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.n.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.c.tdb 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.c.tdb 30: Analysing hydrogen-bonding network for automated assignment of histidine 30: protonation. 14 donors and 15 acceptors were found. 30: There are 20 hydrogen bonds 30: Will use HISE for residue 8 30: 8 out of 8 lines of specbond.dat converted successfully 30: Special Atom Distance matrix: 30: CYS3 HIS8 30: SG9 NE251 30: HIS8 NE251 1.055 30: MET12 SD83 0.763 0.990 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 173, now 173 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 441 pairs 30: Before cleaning: 446 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 9 cmap torsion pairs 30: There are 446 dihedrals, 29 impropers, 312 angles 30: 438 pairs, 173 bonds and 0 virtual sites 30: Total mass 1262.488 a.m.u. 30: Total charge -1.000 e 30: Writing topology 30: 8 out of 8 lines of specbond.dat converted successfully 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/aminoacids.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/dna.arn 30: Opening force field file /build/gromacs-2019.1/share/top/charmm27.ff/rna.arn 30: Making bonds... 30: Number of bonds was 83, now 83 30: Generating angles, dihedrals and pairs... 30: Before cleaning: 211 pairs 30: Before cleaning: 216 dihedrals 30: Keeping all generated dihedrals 30: Making cmap torsions... 30: There are 3 cmap torsion pairs 30: There are 216 dihedrals, 18 impropers, 148 angles 30: 211 pairs, 83 bonds and 0 virtual sites 30: Total mass 601.643 a.m.u. 30: Total charge 1.000 e 30: Writing topology 30: Now there are 255 atoms and 16 residues 30: Total mass in system 1864.131 a.m.u. 30: Total charge in system 0.000 e 30: 30: Writing coordinate file... 30: 30: Using the Charmm27 force field in directory charmm27.ff 30: 30: going to rename charmm27.ff/aminoacids.r2b 30: going to rename charmm27.ff/rna.r2b 30: Reading /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb... 30: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms 30: Analyzing pdb file 30: Splitting chemical chains based on TER records and chain id changing. 30: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms 30: 30: chain #res #atoms 30: 1 'A' 11 86 30: 2 'C' 5 41 30: 30: Reading residue database... (Charmm27) 30: Processing chain 1 'A' (86 atoms, 11 residues) 30: Identified residue ALA2 as a starting terminus. 30: Identified residue MET12 as a ending terminus. 30: Start terminus ALA-2: NH3+ 30: End terminus MET-12: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 11 residues with 172 atoms 30: Chain time... 30: Processing chain 2 'C' (41 atoms, 5 residues) 30: Identified residue ASN13 as a starting terminus. 30: Identified residue SER17 as a ending terminus. 30: Start terminus ASN-13: NH3+ 30: End terminus SER-17: COO- 30: Checking for duplicate atoms.... 30: Generating any missing hydrogen atoms and/or adding termini. 30: Now there are 5 residues with 83 atoms 30: Chain time... 30: Including chain 1 in system: 172 atoms 11 residues 30: Including chain 2 in system: 83 atoms 5 residues 30: --------- PLEASE NOTE ------------ 30: You have successfully generated a topology from: /build/gromacs-2019.1/src/gromacs/gmxpreprocess/tests/chainTer.pdb. 30: The Charmm27 force field and the tip3p water model are used. 30: --------- ETON ESAELP ------------ 30: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (83 ms) 30: [----------] 8 tests from ChainSep/Pdb2gmxTest (2322 ms total) 30: 30: [----------] Global test environment tear-down 30: [==========] 80 tests from 6 test cases ran. (30969 ms total) 30: [ PASSED ] 80 tests. 30/40 Test #30: Pdb2gmxTest ...................... Passed 31.02 sec test 31 Start 31: CorrelationsTest 31: Test command: /build/gromacs-2019.1/build/basic-dp/bin/correlations-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/CorrelationsTest.xml" 31: Test timeout computed to be: 30 31: [==========] Running 11 tests from 2 test cases. 31: [----------] Global test environment set-up. 31: [----------] 10 tests from AutocorrTest 31: [ RUN ] AutocorrTest.EacNormal 31: [ OK ] AutocorrTest.EacNormal (31 ms) 31: [ RUN ] AutocorrTest.EacNoNormalize 31: [ OK ] AutocorrTest.EacNoNormalize (16 ms) 31: [ RUN ] AutocorrTest.EacCos 31: [ OK ] AutocorrTest.EacCos (60 ms) 31: [ RUN ] AutocorrTest.EacVector 31: [ OK ] AutocorrTest.EacVector (24 ms) 31: [ RUN ] AutocorrTest.EacRcross 31: [ OK ] AutocorrTest.EacRcross (2 ms) 31: [ RUN ] AutocorrTest.EacP0 31: [ OK ] AutocorrTest.EacP0 (21 ms) 31: [ RUN ] AutocorrTest.EacP1 31: [ OK ] AutocorrTest.EacP1 (28 ms) 31: [ RUN ] AutocorrTest.EacP2 31: [ OK ] AutocorrTest.EacP2 (52 ms) 31: [ RUN ] AutocorrTest.EacP3 31: [ OK ] AutocorrTest.EacP3 (7 ms) 31: [ RUN ] AutocorrTest.EacP4 31: [ OK ] AutocorrTest.EacP4 (25 ms) 31: [----------] 10 tests from AutocorrTest (267 ms total) 31: 31: [----------] 1 test from ManyAutocorrelationTest 31: [ RUN ] ManyAutocorrelationTest.Empty 31: [ OK ] ManyAutocorrelationTest.Empty (1 ms) 31: [----------] 1 test from ManyAutocorrelationTest (1 ms total) 31: 31: [----------] Global test environment tear-down 31: [==========] 11 tests from 2 test cases ran. (274 ms total) 31: [ PASSED ] 11 tests. 31/40 Test #31: CorrelationsTest ................. Passed 0.30 sec test 32 Start 32: AnalysisDataUnitTests 32: Test command: /build/gromacs-2019.1/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml" 32: Test timeout computed to be: 30 32: [==========] Running 69 tests from 14 test cases. 32: [----------] Global test environment set-up. 32: [----------] 3 tests from AnalysisDataInitializationTest 32: [ RUN ] AnalysisDataInitializationTest.BasicInitialization 32: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (0 ms) 32: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules 32: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms) 32: [----------] 3 tests from AnalysisDataInitializationTest (0 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (0 ms) 32: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (0 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/0 (7 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (0 ms) 32: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/1 (8 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (2 ms) 32: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (0 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/2 (9 ms total) 32: 32: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly 32: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (2 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames 32: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData 32: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (1 ms) 32: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks 32: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (1 ms) 32: [----------] 8 tests from AnalysisDataCommonTest/3 (10 ms total) 32: 32: [----------] 4 tests from AnalysisArrayDataTest 32: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly 32: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (1 ms) 32: [ RUN ] AnalysisArrayDataTest.StorageWorks 32: [ OK ] AnalysisArrayDataTest.StorageWorks (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxis 32: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms) 32: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount 32: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms) 32: [----------] 4 tests from AnalysisArrayDataTest (1 ms total) 32: 32: [----------] 6 tests from AverageModuleTest 32: [ RUN ] AverageModuleTest.BasicTest 32: [ OK ] AverageModuleTest.BasicTest (2 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipointData 32: [ OK ] AverageModuleTest.HandlesMultipointData (2 ms) 32: [ RUN ] AverageModuleTest.HandlesMultipleDataSets 32: [ OK ] AverageModuleTest.HandlesMultipleDataSets (1 ms) 32: [ RUN ] AverageModuleTest.HandlesDataSetAveraging 32: [ OK ] AverageModuleTest.HandlesDataSetAveraging (2 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeXAxis 32: [ OK ] AverageModuleTest.CanCustomizeXAxis (2 ms) 32: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis 32: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (1 ms) 32: [----------] 6 tests from AverageModuleTest (10 ms total) 32: 32: [----------] 2 tests from FrameAverageModuleTest 32: [ RUN ] FrameAverageModuleTest.BasicTest 32: [ OK ] FrameAverageModuleTest.BasicTest (1 ms) 32: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (2 ms) 32: [----------] 2 tests from FrameAverageModuleTest (3 ms total) 32: 32: [----------] 7 tests from AnalysisHistogramSettingsTest 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms) 32: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange 32: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms) 32: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total) 32: 32: [----------] 2 tests from SimpleHistogramModuleTest 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (3 ms) 32: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 32: [----------] 2 tests from SimpleHistogramModuleTest (5 ms total) 32: 32: [----------] 3 tests from WeightedHistogramModuleTest 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (3 ms) 32: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll 32: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (2 ms) 32: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets 32: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (2 ms) 32: [----------] 3 tests from WeightedHistogramModuleTest (8 ms total) 32: 32: [----------] 3 tests from BinAverageModuleTest 32: [ RUN ] BinAverageModuleTest.ComputesCorrectly 32: [ OK ] BinAverageModuleTest.ComputesCorrectly (2 ms) 32: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll 32: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (1 ms) 32: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets 32: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (2 ms) 32: [----------] 3 tests from BinAverageModuleTest (5 ms total) 32: 32: [----------] 4 tests from AbstractAverageHistogramTest 32: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly 32: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (3 ms) 32: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram 32: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (2 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (2 ms) 32: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins 32: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (2 ms) 32: [----------] 4 tests from AbstractAverageHistogramTest (9 ms total) 32: 32: [----------] 3 tests from LifetimeModuleTest 32: [ RUN ] LifetimeModuleTest.BasicTest 32: [ OK ] LifetimeModuleTest.BasicTest (2 ms) 32: [ RUN ] LifetimeModuleTest.CumulativeTest 32: [ OK ] LifetimeModuleTest.CumulativeTest (1 ms) 32: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets 32: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (2 ms) 32: [----------] 3 tests from LifetimeModuleTest (5 ms total) 32: 32: [----------] Global test environment tear-down 32: [==========] 69 tests from 14 test cases ran. (80 ms total) 32: [ PASSED ] 69 tests. 32/40 Test #32: AnalysisDataUnitTests ............ Passed 0.10 sec test 33 Start 33: SelectionUnitTests 33: Test command: /build/gromacs-2019.1/build/basic-dp/bin/selection-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml" 33: Test timeout computed to be: 30 33: [==========] Running 190 tests from 10 test cases. 33: [----------] Global test environment set-up. 33: [----------] 1 test from IndexGroupTest 33: [ RUN ] IndexGroupTest.RemovesDuplicates 33: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms) 33: [----------] 1 test from IndexGroupTest (0 ms total) 33: 33: [----------] 15 tests from IndexBlockTest 33: [ RUN ] IndexBlockTest.CreatesUnknownBlock 33: [ OK ] IndexBlockTest.CreatesUnknownBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesAtomBlock 33: [ OK ] IndexBlockTest.CreatesAtomBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlock 33: [ OK ] IndexBlockTest.CreatesResidueBlock (0 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlock 33: [ OK ] IndexBlockTest.CreatesMoleculeBlock (1 ms) 33: [ RUN ] IndexBlockTest.CreatesResidueBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesResidueBlockWithCompletion (0 ms) 33: [ RUN ] IndexBlockTest.CreatesMoleculeBlockWithCompletion 33: [ OK ] IndexBlockTest.CreatesMoleculeBlockWithCompletion (0 ms) 33: [ RUN ] IndexBlockTest.CreatesSingleBlock 33: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms) 33: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive 33: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative 33: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms) 33: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative 33: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms) 33: [----------] 15 tests from IndexBlockTest (2 ms total) 33: 33: [----------] 11 tests from IndexMapTest 33: [ RUN ] IndexMapTest.InitializesAtomBlock 33: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle 33: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue 33: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule 33: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (0 ms) 33: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll 33: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms) 33: [ RUN ] IndexMapTest.InitializesMoleculeBlock 33: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms) 33: [ RUN ] IndexMapTest.MapsSingleBlock 33: [ OK ] IndexMapTest.MapsSingleBlock (0 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocks 33: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms) 33: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask 33: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (0 ms) 33: [ RUN ] IndexMapTest.HandlesMultipleRequests 33: [ OK ] IndexMapTest.HandlesMultipleRequests (1 ms) 33: [----------] 11 tests from IndexMapTest (5 ms total) 33: 33: [----------] 15 tests from NeighborhoodSearchTest 33: [ RUN ] NeighborhoodSearchTest.SimpleSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSearch (24 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY 33: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (27 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchBox 33: [ OK ] NeighborhoodSearchTest.GridSearchBox (5 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic 33: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (14 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC 33: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (9 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC 33: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (4 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox 33: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (5 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (0 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch 33: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (74 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches 33: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC 33: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms) 33: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs 33: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms) 33: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions 33: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (6 ms) 33: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions 33: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (1 ms) 33: [----------] 15 tests from NeighborhoodSearchTest (169 ms total) 33: 33: [----------] 12 tests from PositionCalculationTest 33: [ RUN ] PositionCalculationTest.ComputesAtomPositions 33: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions 33: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions 33: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (0 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax 33: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms) 33: [ RUN ] PositionCalculationTest.ComputesPositionMask 33: [ OK ] PositionCalculationTest.ComputesPositionMask (0 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (0 ms) 33: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2 33: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (0 ms) 33: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms) 33: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations 33: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (0 ms) 33: [----------] 12 tests from PositionCalculationTest (6 ms total) 33: 33: [----------] 30 tests from SelectionCollectionTest 33: [ RUN ] SelectionCollectionTest.HandlesNoSelections 33: [ OK ] SelectionCollectionTest.HandlesNoSelections (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType 33: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests 33: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry 33: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms) 33: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile 33: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace 33: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions 33: [ OK ] SelectionCollectionTest.HandlesUnsupportedRegularExpressions (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3 33: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 33: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms) 33: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed 33: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 33: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes 33: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo 33: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (0 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms) 33: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3 33: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (0 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms) 33: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 33: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (1 ms) 33: [----------] 30 tests from SelectionCollectionTest (22 ms total) 33: 33: [----------] 14 tests from SelectionCollectionInteractiveTest 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation 33: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (0 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (2 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections 33: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine 33: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (0 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput 33: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (1 ms) 33: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively 33: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms) 33: [----------] 14 tests from SelectionCollectionInteractiveTest (13 ms total) 33: 33: [----------] 66 tests from SelectionCollectionDataTest 33: [ RUN ] SelectionCollectionDataTest.HandlesAllNone 33: [ OK ] SelectionCollectionDataTest.HandlesAllNone (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr 33: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResnr 33: [ OK ] SelectionCollectionDataTest.HandlesResnr (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResIndex 33: [ OK ] SelectionCollectionDataTest.HandlesResIndex (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex 33: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesAtomname (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname 33: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype 33: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesChain 33: [ OK ] SelectionCollectionDataTest.HandlesChain (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMass 33: [ OK ] SelectionCollectionDataTest.HandlesMass (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCharge 33: [ OK ] SelectionCollectionDataTest.HandlesCharge (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc 33: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode 33: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy 33: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBeta 33: [ OK ] SelectionCollectionDataTest.HandlesBeta (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesResname 33: [ OK ] SelectionCollectionDataTest.HandlesResname (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName 33: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword 33: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (6 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (4 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier 33: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (3 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (2 ms) 33: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology 33: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets 33: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames 33: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed 33: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions 33: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (0 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges 33: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode 33: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching 33: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching 33: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean 33: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters 33: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame 33: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods 33: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic 33: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons 33: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions 33: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables 33: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (3 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier 33: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable 33: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables 33: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables 33: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables 33: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (1 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (2 ms) 33: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 33: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (1 ms) 33: [----------] 66 tests from SelectionCollectionDataTest (107 ms total) 33: 33: [----------] 17 tests from SelectionOptionTest 33: [ RUN ] SelectionOptionTest.ParsesSimpleSelection 33: [ OK ] SelectionOptionTest.ParsesSimpleSelection (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired 33: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired 33: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired 33: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (1 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptySelections 33: [ OK ] SelectionOptionTest.ChecksEmptySelections (0 ms) 33: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections 33: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelections 33: [ OK ] SelectionOptionTest.HandlesTooManySelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText 33: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesAdjuster 33: [ OK ] SelectionOptionTest.HandlesAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections 33: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (0 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection 33: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms) 33: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster 33: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (0 ms) 33: [----------] 17 tests from SelectionOptionTest (9 ms total) 33: 33: [----------] 9 tests from SelectionFileOptionTest 33: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions 33: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet 33: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (0 ms) 33: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile 33: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (0 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile 33: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms) 33: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles 33: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms) 33: [----------] 9 tests from SelectionFileOptionTest (6 ms total) 33: 33: [----------] Global test environment tear-down 33: [==========] 190 tests from 10 test cases ran. (340 ms total) 33: [ PASSED ] 190 tests. 33/40 Test #33: SelectionUnitTests ............... Passed 0.37 sec test 34 Start 34: TrajectoryAnalysisUnitTests 34: Test command: /build/gromacs-2019.1/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml" 34: Test timeout computed to be: 30 34: [==========] Running 74 tests from 14 test cases. 34: [----------] Global test environment set-up. 34: [----------] 5 tests from ClustsizeTest 34: [ RUN ] ClustsizeTest.NoMolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 2, cmax: 4, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (4 ms) 34: [ RUN ] ClustsizeTest.NoMolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements 34: There is one group in the index 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 24 34: cmid: 1, cmax: 6, max_size: 6 34: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6 34: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (3 ms) 34: [ RUN ] ClustsizeTest.MolDefaultCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (3 ms) 34: [ RUN ] ClustsizeTest.MolShortCutoff 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 1, cmax: 6, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (4 ms) 34: [ RUN ] ClustsizeTest.MolCSize 34: Reading frames from pdb file Reading frame 0 time 0.000 Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision) 34: '', 24 atoms 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Total number of atoms in clusters = 8 34: cmid: 2, cmax: 4, max_size: 2 34: 50%100%cmid: 2, cmax: 6, max_size: 2 34: 50%100%[ OK ] ClustsizeTest.MolCSize (4 ms) 34: [----------] 5 tests from ClustsizeTest (18 ms total) 34: 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (1 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (5 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset 34: Reading frames from gro file 'Test system', 8 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (6 ms) 34: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory 34: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (1 ms) 34: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (13 ms total) 34: 34: [----------] 11 tests from AngleModuleTest 34: [ RUN ] AngleModuleTest.ComputesSimpleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesSimpleAngles (6 ms) 34: [ RUN ] AngleModuleTest.ComputesDihedrals 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesDihedrals (6 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPairAngles (6 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (7 ms) 34: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (5 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (7 ms) 34: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles 34: Reading frames from gro file 'Test system for different angles', 33 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (6 ms) 34: [ RUN ] AngleModuleTest.ComputesMultipleAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.ComputesMultipleAngles (6 ms) 34: [ RUN ] AngleModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesDynamicSelections (6 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (6 ms) 34: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (7 ms) 34: [----------] 11 tests from AngleModuleTest (69 ms total) 34: 34: [----------] 3 tests from DistanceModuleTest 34: [ RUN ] DistanceModuleTest.ComputesDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: [ OK ] DistanceModuleTest.ComputesDistances (7 ms) 34: [ RUN ] DistanceModuleTest.ComputesMultipleDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2: 34: Number of samples: 5 34: Average distance: 1.43246 nm 34: Standard deviation: 0.96700 nm 34: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB: 34: Number of samples: 4 34: Average distance: 1.81066 nm 34: Standard deviation: 0.79289 nm 34: [ OK ] DistanceModuleTest.ComputesMultipleDistances (8 ms) 34: [ RUN ] DistanceModuleTest.HandlesDynamicSelections 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: atomname S1 S2 and res_cog x < 2.8: 34: Number of samples: 3 34: Average distance: 1.72076 nm 34: Standard deviation: 1.24839 nm 34: [ OK ] DistanceModuleTest.HandlesDynamicSelections (8 ms) 34: [----------] 3 tests from DistanceModuleTest (23 ms total) 34: 34: [----------] 2 tests from FreeVolumeModuleTest 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for CO2-RM. Set to zero. 34: Could not determine VDW radius for 40 particles. These were set to zero. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 13 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.02 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3 34: Fractional free volume 0.194 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (215 ms) 34: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: Reading file /build/gromacs-2019.1/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision) 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: cutoff = 0.18 nm 34: probe_radius = 0 nm 34: seed = 17 34: ninsert = 1000 probes per nm^3 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David 34: van der Spoel and Luciano T. Costa 34: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium 34: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View 34: Environ. Sci. Technol. 47 (2013) pp. 7421-7429 34: -------- -------- --- Thank You --- -------- -------- 34: 34: Free volume 38.48 +/- 0.00 % 34: Total volume 68.92 +/- 0.00 nm^3 34: Number of molecules 340 total mass 63491.38 Dalton 34: Average molar mass: 186.74 Dalton 34: Density rho: 1529.71 +/- 0.00 nm^3 34: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3 34: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3 34: Fractional free volume 0.200 +/- 0.000 34: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (212 ms) 34: [----------] 2 tests from FreeVolumeModuleTest (427 ms total) 34: 34: [----------] 7 tests from PairDistanceModuleTest 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistances 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistances (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (6 ms) 34: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (6 ms) 34: [----------] 7 tests from PairDistanceModuleTest (42 ms total) 34: 34: [----------] 5 tests from RdfModuleTest 34: [ RUN ] RdfModuleTest.BasicTest 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.BasicTest (43 ms) 34: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork 34: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms. 34: Reading frame 0 time 0.000 Last frame 0 time 0.000 34: Analyzed 1 frames, last time 0.000 34: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (32 ms) 34: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (42 ms) 34: [ RUN ] RdfModuleTest.CalculatesSurf 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesSurf (21 ms) 34: [ RUN ] RdfModuleTest.CalculatesXY 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] RdfModuleTest.CalculatesXY (50 ms) 34: [----------] 5 tests from RdfModuleTest (190 ms total) 34: 34: [----------] 5 tests from SasaModuleTest 34: [ RUN ] SasaModuleTest.BasicTest 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.BasicTest (22 ms) 34: [ RUN ] SasaModuleTest.HandlesSelectedResidues 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesSelectedResidues (14 ms) 34: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (12 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (16 ms) 34: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and 34: Michael Scharf 34: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration 34: of Surface Area and Volume and to Dot Surface Contouring of Molecular 34: Assemblies 34: J. Comp. Chem. 16 (1995) pp. 273-284 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii 34: from the source below. This means the results may be different 34: compared to previous GROMACS versions. 34: 34: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ 34: A. Bondi 34: van der Waals Volumes and Radii 34: J. Phys. Chem. 68 (1964) pp. 441-451 34: -------- -------- --- Thank You --- -------- -------- 34: 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (15 ms) 34: [----------] 5 tests from SasaModuleTest (81 ms total) 34: 34: [----------] 8 tests from SelectModuleTest 34: [ RUN ] SelectModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.BasicTest (9 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (8 ms) 34: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (8 ms) 34: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (8 ms) 34: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (8 ms) 34: [ RUN ] SelectModuleTest.NormalizesSizes 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.NormalizesSizes (6 ms) 34: [ RUN ] SelectModuleTest.WritesResidueNumbers 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueNumbers (5 ms) 34: [ RUN ] SelectModuleTest.WritesResidueIndices 34: 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Analyzed topology coordinates 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] SelectModuleTest.WritesResidueIndices (5 ms) 34: [----------] 8 tests from SelectModuleTest (59 ms total) 34: 34: [----------] 10 tests from SurfaceAreaTest 34: [ RUN ] SurfaceAreaTest.ComputesSinglePoint 34: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPoints 34: [ OK ] SurfaceAreaTest.ComputesTwoPoints (2 ms) 34: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius 34: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (2 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints12 34: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints32 34: [ OK ] SurfaceAreaTest.SurfacePoints32 (0 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints42 34: [ OK ] SurfaceAreaTest.SurfacePoints42 (1 ms) 34: [ RUN ] SurfaceAreaTest.SurfacePoints122 34: [ OK ] SurfaceAreaTest.SurfacePoints122 (1 ms) 34: [ RUN ] SurfaceAreaTest.Computes100Points 34: [ OK ] SurfaceAreaTest.Computes100Points (1 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (4 ms) 34: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC 34: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (5 ms) 34: [----------] 10 tests from SurfaceAreaTest (18 ms total) 34: 34: [----------] 4 tests from TopologyInformation 34: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile 34: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (1 ms) 34: [ RUN ] TopologyInformation.WorksWithGroFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithGroFile (5 ms) 34: [ RUN ] TopologyInformation.WorksWithPdbFile 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TopologyInformation.WorksWithPdbFile (5 ms) 34: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile 34: 34: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp, line 1]: 34: /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 34: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 34: scheme was introduced, but the group scheme was still the default. The 34: default is now the Verlet scheme, so you will observe different behaviour. 34: 34: 34: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: For a correct single-point energy evaluation with nsteps = 0, use 34: continuation = yes to avoid constraining the input coordinates. 34: 34: Setting the LD random seed to -1859738169 34: Generated 330891 of the 330891 non-bonded parameter combinations 34: Generating 1-4 interactions: fudge = 0.5 34: Generated 330891 of the 330891 1-4 parameter combinations 34: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 34: 34: NOTE 3 [file lysozyme.top, line 1465]: 34: System has non-zero total charge: 2.000000 34: Total charge should normally be an integer. See 34: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 34: for discussion on how close it should be to an integer. 34: 34: 34: 34: Removing all charge groups because cutoff-scheme=Verlet 34: Number of degrees of freedom in T-Coupling group rest is 465.00 34: 34: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: NVE simulation with an initial temperature of zero: will use a Verlet 34: buffer of 10%. Check your energy drift! 34: 34: 34: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]: 34: You are using a plain Coulomb cut-off, which might produce artifacts. 34: You might want to consider using PME electrostatics. 34: 34: 34: 34: There were 5 notes 34: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (double precision) 34: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2019.1 (double precision) 34: Analysing residue names: 34: There are: 10 Protein residues 34: Analysing Protein... 34: This run will generate roughly 0 Mb of data 34: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (446 ms) 34: [----------] 4 tests from TopologyInformation (458 ms total) 34: 34: [----------] 4 tests from TrajectoryModuleTest 34: [ RUN ] TrajectoryModuleTest.BasicTest 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.BasicTest (6 ms) 34: [ RUN ] TrajectoryModuleTest.PlotsXOnly 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.PlotsXOnly (7 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (6 ms) 34: [ RUN ] TrajectoryModuleTest.HandlesNoForces 34: Reading frames from gro file 'Test system', 15 atoms. 34: Reading frame 0 time 0.000 34: WARNING: If there are molecules in the input trajectory file 34: that are broken across periodic boundaries, they 34: cannot be made whole (or treated as whole) without 34: you providing a run input file. 34: 34: Reading frame 1 time 0.000 Last frame 1 time 0.000 34: Analyzed 2 frames, last time 0.000 34: 34: WARNING: Masses and atomic (Van der Waals) radii will be guessed 34: based on residue and atom names, since they could not be 34: definitively assigned from the information in your input 34: files. These guessed numbers might deviate from the mass 34: and radius of the atom type. Please check the output 34: files if necessary. 34: 34: [ OK ] TrajectoryModuleTest.HandlesNoForces (6 ms) 34: [----------] 4 tests from TrajectoryModuleTest (25 ms total) 34: 34: [----------] 5 tests from UnionFinderTest 34: [ RUN ] UnionFinderTest.WorksEmpty 34: [ OK ] UnionFinderTest.WorksEmpty (0 ms) 34: [ RUN ] UnionFinderTest.BasicMerges 34: [ OK ] UnionFinderTest.BasicMerges (1 ms) 34: [ RUN ] UnionFinderTest.LargerMerges 34: [ OK ] UnionFinderTest.LargerMerges (0 ms) 34: [ RUN ] UnionFinderTest.LongRightMerge 34: [ OK ] UnionFinderTest.LongRightMerge (0 ms) 34: [ RUN ] UnionFinderTest.LongLeftMerge 34: [ OK ] UnionFinderTest.LongLeftMerge (0 ms) 34: [----------] 5 tests from UnionFinderTest (1 ms total) 34: 34: [----------] 1 test from MappedUnionFinderTest 34: [ RUN ] MappedUnionFinderTest.BasicMerges 34: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms) 34: [----------] 1 test from MappedUnionFinderTest (0 ms total) 34: 34: [----------] Global test environment tear-down 34: [==========] 74 tests from 14 test cases ran. (1425 ms total) 34: [ PASSED ] 74 tests. 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 1.45 sec test 35 Start 35: EnergyAnalysisUnitTests 35: Test command: /build/gromacs-2019.1/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml" 35: Test timeout computed to be: 30 35: [==========] Running 7 tests from 4 test cases. 35: [----------] Global test environment set-up. 35: [----------] 1 test from DhdlTest 35: [ RUN ] DhdlTest.ExtractDhdl 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision) 35: Note: file tpx version 110, software tpx version 116 35: 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 35: 35: 35: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /build/gromacs-2019.1/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg 35: [ OK ] DhdlTest.ExtractDhdl (16 ms) 35: [----------] 1 test from DhdlTest (16 ms total) 35: 35: [----------] 1 test from OriresTest 35: [ RUN ] OriresTest.ExtractOrires 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file 35: Reading file /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision) 35: Note: file tpx version 111, software tpx version 116 35: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all) 35: End your selection with 0 35: Selecting all 7 orientation restraints 35: 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 35: [ OK ] OriresTest.ExtractOrires (17 ms) 35: [----------] 1 test from OriresTest (17 ms total) 35: 35: [----------] 3 tests from EnergyTest 35: [ RUN ] EnergyTest.ExtractEnergy 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Potential -34142.2 39 228.993 -62.8906 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: [ OK ] EnergyTest.ExtractEnergy (5 ms) 35: [ RUN ] EnergyTest.ExtractEnergyByNumber 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol) 35: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol) 35: Pres. DC -268.49 3 8.52175 13.2804 (bar) 35: [ OK ] EnergyTest.ExtractEnergyByNumber (4 ms) 35: [ RUN ] EnergyTest.ExtractEnergyMixed 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 35: Select the terms you want from the following list by 35: selecting either (part of) the name or the number or a combination. 35: End your selection with an empty line or a zero. 35: ------------------------------------------------------------------- 35: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip. 35: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature 35: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y 35: 13 Box-Z 14 Volume 15 Density 16 pV 35: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ 35: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX 35: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY 35: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ 35: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen 35: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System 35: 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: [ OK ] EnergyTest.ExtractEnergyMixed (5 ms) 35: [----------] 3 tests from EnergyTest (16 ms total) 35: 35: [----------] 2 tests from ViscosityTest 35: [ RUN ] ViscosityTest.EinsteinViscosity 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosity (66 ms) 35: [ RUN ] ViscosityTest.EinsteinViscosityIntegral 35: Opened /build/gromacs-2019.1/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file 35: 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 35: 35: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets 35: All statistics are over 5001 points 35: 35: Energy Average Err.Est. RMSD Tot-Drift 35: ------------------------------------------------------------------------------- 35: Pres-XX 20.2092 65 717.193 185.978 (bar) 35: Pres-XY -47.7351 39 372.522 207.456 (bar) 35: Pres-XZ 11.477 31 379.79 6.80818 (bar) 35: Pres-YX -47.7106 39 372.525 207.5 (bar) 35: Pres-YY 38.9241 40 803.899 -27.1505 (bar) 35: Pres-YZ -41.3534 45 401.216 114.663 (bar) 35: Pres-ZX 11.5238 31 379.804 6.91707 (bar) 35: Pres-ZY -41.3119 45 401.196 114.743 (bar) 35: Pres-ZZ -43.1021 63 748.522 -173.491 (bar) 35: Temperature 300.001 0.02 5.8425 -0.0130558 (K) 35: Volume 25.0162 0.14 0.386769 0.598615 (nm^3) 35: Pressure 5.34371 4.1 605.307 -4.88771 (bar) 35: [ OK ] ViscosityTest.EinsteinViscosityIntegral (60 ms) 35: [----------] 2 tests from ViscosityTest (126 ms total) 35: 35: [----------] Global test environment tear-down 35: [==========] 7 tests from 4 test cases ran. (175 ms total) 35: [ PASSED ] 7 tests. 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.20 sec test 36 Start 36: ToolUnitTests 36: Test command: /build/gromacs-2019.1/build/basic-dp/bin/tool-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/ToolUnitTests.xml" 36: Test timeout computed to be: 30 36: [==========] Running 4 tests from 1 test case. 36: [----------] Global test environment set-up. 36: [----------] 4 tests from ReportMethodsTest 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted 36: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms) 36: [ RUN ] ReportMethodsTest.WritesCorrectInformation 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to 84089614 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_WritesCorrectInformation_lysozyme.tpr, VERSION 2019.1 (double precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: [ OK ] ReportMethodsTest.WritesCorrectInformation (471 ms) 36: [ RUN ] ReportMethodsTest.ToolEndToEndTest 36: 36: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp, line 1]: 36: /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 36: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 36: scheme was introduced, but the group scheme was still the default. The 36: default is now the Verlet scheme, so you will observe different behaviour. 36: 36: 36: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: For a correct single-point energy evaluation with nsteps = 0, use 36: continuation = yes to avoid constraining the input coordinates. 36: 36: Setting the LD random seed to -1826422551 36: Generated 330891 of the 330891 non-bonded parameter combinations 36: Generating 1-4 interactions: fudge = 0.5 36: Generated 330891 of the 330891 1-4 parameter combinations 36: Excluding 3 bonded neighbours molecule type 'Protein_chain_B' 36: 36: NOTE 3 [file lysozyme.top, line 1465]: 36: System has non-zero total charge: 2.000000 36: Total charge should normally be an integer. See 36: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic 36: for discussion on how close it should be to an integer. 36: 36: 36: 36: Removing all charge groups because cutoff-scheme=Verlet 36: Number of degrees of freedom in T-Coupling group rest is 465.00 36: 36: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: NVE simulation with an initial temperature of zero: will use a Verlet 36: buffer of 10%. Check your energy drift! 36: 36: 36: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.mdp]: 36: You are using a plain Coulomb cut-off, which might produce artifacts. 36: You might want to consider using PME electrostatics. 36: 36: 36: 36: There were 5 notes 36: Reading file /build/gromacs-2019.1/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_ToolEndToEndTest_lysozyme.tpr, VERSION 2019.1 (double precision) 36: Analysing residue names: 36: There are: 10 Protein residues 36: Analysing Protein... 36: This run will generate roughly 0 Mb of data 36: section: Methods 36: subsection: Simulation system 36: A system of 1 molecules (156 atoms) was simulated. 36: 36: subsection: Simulation settings 36: A total of 0 ns were simulated with a time step of 1 fs. 36: Neighbor searching was performed every 10 steps. 36: The Cut-off algorithm was used for electrostatic interactions. 36: with a cut-off of 1 nm. 36: A single cut-off of 1.1 nm was used for Van der Waals interactions. 36: [ OK ] ReportMethodsTest.ToolEndToEndTest (433 ms) 36: [----------] 4 tests from ReportMethodsTest (904 ms total) 36: 36: [----------] Global test environment tear-down 36: [==========] 4 tests from 1 test case ran. (904 ms total) 36: [ PASSED ] 4 tests. 36/40 Test #36: ToolUnitTests .................... Passed 0.93 sec test 37 Start 37: MdrunTests 37: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunTests.xml" 37: Test timeout computed to be: 600 37: [==========] Running 29 tests from 11 test cases. 37: [----------] Global test environment set-up. 37: [----------] 1 test from GromppTest 37: [ RUN ] GromppTest.EmptyMdpFileWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -494954693 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] GromppTest.EmptyMdpFileWorks (41 ms) 37: [----------] 1 test from GromppTest (41 ms total) 37: 37: [----------] 1 test from ImdTest 37: [ RUN ] ImdTest.ImdCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to -1830699459 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Group 'SecondWaterMolecule' with 3 atoms can be activated for interactive molecular dynamics (IMD). 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/ImdTest_ImdCanRun.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.126 to 1.358 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: IMD: Enabled. This simulation will accept incoming IMD connections. 37: IMD: You chose a port number < 1. Will automatically assign a free port. 37: IMD: Pulling from IMD remote is enabled (-imdpull). 37: IMD: Turning on IMD - port for incoming requests is 0. 37: IMD: Setting up incoming socket. 37: IMD: Listening for IMD connection on port 53053. 37: IMD: -imdwait not set, starting simulation. 37: starting mdrun 'spc2' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.134 nm, buffer size 0.134 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.121 nm, buffer size 0.121 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 67 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.014 0.007 197.8 37: (ns/day) (hour/ns) 37: Performance: 146.661 0.164 37: [ OK ] ImdTest.ImdCanRun (56 ms) 37: [----------] 1 test from ImdTest (56 ms total) 37: 37: [----------] 2 tests from PmeTest 37: [ RUN ] PmeTest.ReproducesEnergies 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -118108882 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: NVE simulation: will use the initial temperature of 1046.791 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.080 0.040 199.6 37: (ns/day) (hour/ns) 37: Performance: 45.308 0.530 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 37: 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/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.079 0.040 199.6 37: (ns/day) (hour/ns) 37: Performance: 45.657 0.526 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 37: 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/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 20 steps, 0.0 ps. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.080 0.040 199.6 37: (ns/day) (hour/ns) 37: Performance: 45.198 0.531 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 37: 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 ] PmeTest.ReproducesEnergies (271 ms) 37: [ RUN ] PmeTest.ScalesTheBox 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -208123863 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Searching the wall atom type(s) 37: Number of degrees of freedom in T-Coupling group rest is 13.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: NVE simulation: will use the initial temperature of 966.269 K for 37: determining the Verlet buffer size 37: 37: Estimate for the relative computational load of the PME mesh part: 1.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 37: The optimal PME mesh load for parallel simulations is below 0.5 37: and for highly parallel simulations between 0.25 and 0.33, 37: for higher performance, increase the cut-off and the PME grid spacing. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 0 steps, 0.0 ps. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.019 0.009 197.0 37: (ns/day) (hour/ns) 37: Performance: 9.200 2.609 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K 37: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: Calculating fourier grid dimensions for X Y Z 37: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 37: This run will generate roughly 0 Mb of data 37: [ OK ] PmeTest.ScalesTheBox (106 ms) 37: [----------] 2 tests from PmeTest (377 ms total) 37: 37: [----------] 1 test from CompelTest 37: [ RUN ] CompelTest.SwapCanRun 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: The Berendsen thermostat does not generate the correct kinetic energy 37: distribution. You might want to consider using the V-rescale thermostat. 37: 37: Setting the LD random seed to -83091169 37: Generated 330891 of the 330891 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 330891 of the 330891 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 1 bonded neighbours molecule type 'NA' 37: Excluding 1 bonded neighbours molecule type 'CL' 37: Excluding 3 bonded neighbours molecule type 'Protein' 37: Excluding 3 bonded neighbours molecule type 'OCT' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Split0 group 'Ch0' contains 83 atoms. 37: Split1 group 'Ch1' contains 83 atoms. 37: Solvent group 'SOL' contains 11931 atoms. 37: Swap group 'NA+' contains 19 atoms. 37: Swap group 'CL-' contains 19 atoms. 37: Number of degrees of freedom in T-Coupling group System is 27869.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (double precision) 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: SWAP: Determining initial numbers of ions per compartment. 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 2 steps, 0.0 ps. 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: turning all bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K 37: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 1 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 32 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 1.678 0.839 200.0 37: (ns/day) (hour/ns) 37: Performance: 1.544 15.544 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: SWAP: Setting pointers for checkpoint writing 37: SWAP: Copying channel fluxes from checkpoint file data 37: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules 37: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules 37: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules 37: starting mdrun 'Channel_coco in octane membrane' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: NOTE: 30 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.997 0.499 199.9 37: (ns/day) (hour/ns) 37: Performance: 2.599 9.233 37: [ OK ] CompelTest.SwapCanRun (2132 ms) 37: [----------] 1 test from CompelTest (2132 ms total) 37: 37: [----------] 6 tests from BondedInteractionsTest 37: [ RUN ] BondedInteractionsTest.NormalBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -519623426 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 19 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.6 37: (ns/day) (hour/ns) 37: Performance: 179.134 0.134 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalBondWorks (10 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedBondWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -389951019 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 2 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 17 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.7 37: (ns/day) (hour/ns) 37: Performance: 178.253 0.135 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedBondWorks (11 ms) 37: [ RUN ] BondedInteractionsTest.NormalAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 117451210 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 17 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 188.1 37: (ns/day) (hour/ns) 37: Performance: 198.460 0.121 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalAngleWorks (9 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1398619203 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: 37: NOTE 3 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]: 37: In moleculetype 'butane' 1 atoms are not bound by a potential or 37: constraint to any other atom in the same moleculetype. Although 37: technically this might not cause issues in a simulation, this often means 37: that the user forgot to add a bond/potential/constraint or put multiple 37: molecules in the same moleculetype definition by mistake. Run with -v to 37: get information for each atom. 37: 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 18 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 187.6 37: (ns/day) (hour/ns) 37: Performance: 208.869 0.115 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (9 ms) 37: [ RUN ] BondedInteractionsTest.NormalDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1268669887 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 25 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.000 189.8 37: (ns/day) (hour/ns) 37: Performance: 186.126 0.129 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.NormalDihedralWorks (9 ms) 37: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp, line 1]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1672942506 37: Generated 3 of the 3 non-bonded parameter combinations 37: Excluding 3 bonded neighbours molecule type 'butane' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'A single butane', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/butane1.gro' 37: 37: Reading frames from gro file 'A single butane', 4 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 25 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 190.0 37: (ns/day) (hour/ns) 37: Performance: 152.842 0.157 37: This run will generate roughly 0 Mb of data 37: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (12 ms) 37: [----------] 6 tests from BondedInteractionsTest (60 ms total) 37: 37: [----------] 2 tests from MdrunTerminationTest 37: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 1236193846 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 1, rlist from 1.025 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 0: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: NOTE: 70 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 196.6 37: (ns/day) (hour/ns) 37: Performance: 34.843 0.689 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 3 steps, 0.0 ps (continuing from step 1, 0.0 ps). 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.001 190.7 37: (ns/day) (hour/ns) 37: Performance: 181.103 0.133 37: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (19 ms) 37: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp, line 6]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1966764096 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 9.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 1, rlist from 1.025 to 1 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 100 steps, 0.1 ps. 37: 37: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: NOTE: 13 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 190.1 37: (ns/day) (hour/ns) 37: Performance: 167.179 0.144 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksWithNoAppend.tpr, VERSION 2019.1 (double precision) 37: Overriding nsteps with value passed on the command line: 2 steps, 0.002 ps 37: Changing nstlist from 10 to 80, rlist from 1.025 to 1.254 37: 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps). 37: Checkpoint file is from part 1, new output files will be suffixed '.part0002'. 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.001 195.5 37: (ns/day) (hour/ns) 37: Performance: 187.604 0.128 37: [ OK ] MdrunTerminationTest.CheckpointRestartWorksWithNoAppend (21 ms) 37: [----------] 2 tests from MdrunTerminationTest (40 ms total) 37: 37: [----------] 4 tests from MimicTest 37: [ RUN ] MimicTest.OneQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -504874290 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 20 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.001 0.001 191.9 37: (ns/day) (hour/ns) 37: Performance: 125.785 0.191 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.OneQuantumMol (11 ms) 37: [ RUN ] MimicTest.AllQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to 1587375609 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 89 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 198.4 37: (ns/day) (hour/ns) 37: Performance: 16.333 1.469 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.AllQuantumMol (15 ms) 37: [ RUN ] MimicTest.TwoQuantumMol 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -1738361094 37: Generated 10 of the 10 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 10 of the 10 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 21.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: NVE simulation with an initial temperature of zero: will use a Verlet 37: buffer of 10%. Check your energy drift! 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 37: 37: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 38 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 192.6 37: (ns/day) (hour/ns) 37: Performance: 105.776 0.227 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.TwoQuantumMol (10 ms) 37: [ RUN ] MimicTest.BondCuts 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: For a correct single-point energy evaluation with nsteps = 0, use 37: continuation = yes to avoid constraining the input coordinates. 37: 37: Setting the LD random seed to -240714354 37: Generated 2211 of the 2211 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 2211 of the 2211 1-4 parameter combinations 37: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 66.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: NVE simulation: will use the initial temperature of 300.368 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 37: 37: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 37: Reading frame 0 time 0.000 Last frame 0 time 0.000 37: 37: NOTE: 36 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.002 0.001 190.0 37: (ns/day) (hour/ns) 37: Performance: 67.559 0.355 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 37: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: [ OK ] MimicTest.BondCuts (29 ms) 37: [----------] 4 tests from MimicTest (65 ms total) 37: 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 37: Setting the LD random seed to -718829938 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 77 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.016 0.008 197.8 37: (ns/day) (hour/ns) 37: Performance: 21.668 1.108 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (18 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 37: Setting the LD random seed to -2146188969 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 190.4 37: (ns/day) (hour/ns) 37: Performance: 107.390 0.223 37: Reading frame 0 time 0.000 37: # Atoms 6 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (12 ms) 37: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 37: Setting the LD random seed to 936653933 37: Generated 3 of the 3 non-bonded parameter combinations 37: Generating 1-4 interactions: fudge = 0.5 37: Generated 3 of the 3 1-4 parameter combinations 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 9.00 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 2573.591 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc2' 37: 1 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K 37: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.003 0.002 190.8 37: (ns/day) (hour/ns) 37: Performance: 109.087 0.220 37: Reading frame 0 time 0.000 37: # Atoms 3 37: Reading frame 1 time 0.001 Last frame 1 time 0.001 37: 37: 37: Item #frames Timestep (ps) 37: Step 2 0.001 37: Time 2 0.001 37: Lambda 0 37: Coords 2 0.001 37: Velocities 0 37: Forces 0 37: Box 2 0.001 37: Checking file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc 37: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (11 ms) 37: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (41 ms total) 37: 37: [----------] 3 tests from Checking/InitialConstraintsTest 37: [ RUN ] Checking/InitialConstraintsTest.Works/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -179797784 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 18 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.004 0.002 191.6 37: (ns/day) (hour/ns) 37: Performance: 86.221 0.278 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (58 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 406458005 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 3 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 20 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.004 0.002 191.9 37: (ns/day) (hour/ns) 37: Performance: 85.489 0.281 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (50 ms) 37: [ RUN ] Checking/InitialConstraintsTest.Works/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: Integrator method md-vv-avek is implemented primarily for validation 37: purposes; for molecular dynamics, you should probably be using md or md-vv 37: 37: Setting the LD random seed to -768727508 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group rest is 11.00 37: 37: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: NVE simulation: will use the initial temperature of 1141.954 K for 37: determining the Verlet buffer size 37: 37: 37: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 4 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2019.1 (double precision) 37: Can not increase nstlist because an NVE ensemble is used 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 1 steps, 0.0 ps. 37: turning H bonds into constraints... 37: turning H bonds into constraints... 37: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K 37: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 18 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.004 0.002 191.6 37: (ns/day) (hour/ns) 37: Performance: 86.737 0.277 37: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file 37: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (53 ms) 37: [----------] 3 tests from Checking/InitialConstraintsTest (161 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/Trajectories 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 2135068374 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 11 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 196.6 37: (ns/day) (hour/ns) 37: Performance: 113.810 0.211 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (60 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 2086883193 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 196.2 37: (ns/day) (hour/ns) 37: Performance: 123.561 0.194 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (53 ms) 37: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp, line 12]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1733254816 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 6 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.010 0.005 196.4 37: (ns/day) (hour/ns) 37: Performance: 124.489 0.193 37: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (58 ms) 37: [----------] 3 tests from MdrunCanWrite/Trajectories (171 ms total) 37: 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -550651902 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 13 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.006 0.003 193.7 37: (ns/day) (hour/ns) 37: Performance: 90.794 0.264 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (54 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to 608191822 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 13 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.005 0.003 192.9 37: (ns/day) (hour/ns) 37: Performance: 94.306 0.254 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (52 ms) 37: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 37: 37: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp, line 13]: 37: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 37: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 37: scheme was introduced, but the group scheme was still the default. The 37: default is now the Verlet scheme, so you will observe different behaviour. 37: 37: Setting the LD random seed to -1438954507 37: Generated 279 of the 1225 non-bonded parameter combinations 37: Excluding 2 bonded neighbours molecule type 'Methanol' 37: Excluding 2 bonded neighbours molecule type 'SOL' 37: Removing all charge groups because cutoff-scheme=Verlet 37: Number of degrees of freedom in T-Coupling group System is 12.00 37: 37: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]: 37: You are using a plain Coulomb cut-off, which might produce artifacts. 37: You might want to consider using PME electrostatics. 37: 37: 37: 37: There were 2 notes 37: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2019.1 (double precision) 37: Changing nstlist from 10 to 50, rlist from 1.023 to 1.181 37: 37: Using 1 MPI thread 37: Using 2 OpenMP threads 37: 37: 37: NOTE: The number of threads is not equal to the number of (logical) cores 37: and the -pin option is set to auto: will not pin threads to cores. 37: This can lead to significant performance degradation. 37: Consider using -pin on (and -pinoffset in case you run multiple jobs). 37: starting mdrun 'spc-and-methanol' 37: 2 steps, 0.0 ps. 37: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K 37: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm 37: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm 37: Note that mdrun will redetermine rlist based on the actual pair-list setup 37: This run will generate roughly 0 Mb of data 37: 37: Writing final coordinates. 37: 37: NOTE: 12 % of the run time was spent in pair search, 37: you might want to increase nstlist (this has no effect on accuracy) 37: 37: Core t (s) Wall t (s) (%) 37: Time: 0.005 0.003 193.1 37: (ns/day) (hour/ns) 37: Performance: 93.899 0.256 37: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (52 ms) 37: [----------] 3 tests from MdrunCanWrite/NptTrajectories (158 ms total) 37: 37: [----------] Global test environment tear-down 37: [==========] 29 tests from 11 test cases ran. (3303 ms total) 37: [ PASSED ] 29 tests. 37/40 Test #37: MdrunTests ....................... Passed 3.35 sec test 38 Start 38: MdrunNonIntegratorTests 38: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml" 38: Test timeout computed to be: 600 38: [==========] Running 57 tests from 4 test cases. 38: [----------] Global test environment set-up. 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -4.79910464433670e+01 38: Maximum force = 1.86297359800836e+02 on atom 13 38: Norm of force = 8.77219867200401e+01 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (406 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 3.02331e+02 on atom 3 38: F-Norm = 1.18024e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -5.58622539552403e+01 38: Maximum force = 4.27274823589429e+02 on atom 13 38: Norm of force = 1.84530029788115e+02 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (394 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.19376899489616e+02 38: Maximum force = 9.99884921027275e+03 on atom 9 38: Norm of force = 4.61669565061009e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 38: 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 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (213 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: 38: NOTE 3 [file glycine_vacuo.top, line 12]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 22.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41575e+04 on atom 10 38: F-Norm = 1.18451e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.51743017875792e+02 38: Maximum force = 7.42089573427942e+03 on atom 9 38: Norm of force = 3.56929298621805e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 38: 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 turning H bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (187 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.56984194095140e+02 38: Maximum force = 4.56923625858722e+02 on atom 17 38: Norm of force = 1.83258377483269e+02 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 38: 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 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (55 ms) 38: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 3 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: 38: NOTE 4 [file unknown]: 38: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 1.06800e+03 on atom 28 38: F-Norm = 4.26922e+02 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = -1.69410778941233e+02 38: Maximum force = 2.18225948179418e+02 on atom 17 38: Norm of force = 7.92068036007845e+01 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 38: 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 turning all bonds into constraints... 38: This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (70 ms) 38: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1336 ms total) 38: 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents converged to Fmax < 10 in 1 steps 38: Potential Energy = -9.74257075835447e-01 38: Maximum force = 4.01322929015133e+00 on atom 1 38: Norm of force = 1.63839399694378e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (55 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.90642313893957e-01 38: Maximum force = 2.57812909491105e+00 on atom 1 38: Norm of force = 1.05251679559258e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (40 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 2 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 4.01323e+00 on atom 1 38: F-Norm = 1.63839e+00 38: 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 38: Potential Energy = -9.90642313893957e-01 38: Maximum force = 2.57812909491105e+00 on atom 1 38: Norm of force = 1.05251679559258e+00 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (53 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Steepest Descents: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Steepest Descents did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 3.19395484629892e+02 38: Maximum force = 9.97041707215792e+03 on atom 9 38: Norm of force = 4.62274878672162e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (242 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Polak-Ribiere Conjugate Gradients: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.56258793634225e+02 38: Maximum force = 7.50181017498407e+03 on atom 9 38: Norm of force = 3.61390332570590e+03 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (238 ms) 38: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 38: 38: Generated 20503 of the 20503 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 1 38: Generated 17396 of the 20503 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Glycine' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 3 notes 38: 38: There was 1 warning 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: 38: Low-Memory BFGS Minimizer: 38: Tolerance (Fmax) = 1.00000e+01 38: Number of steps = 4 38: Using 10 BFGS correction steps. 38: 38: F-max = 2.41672e+04 on atom 10 38: F-Norm = 1.19357e+04 38: 38: 38: Energy minimization reached the maximum number of steps before the forces 38: reached the requested precision Fmax < 10. 38: 38: writing lowest energy coordinates. 38: 38: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 38: Potential Energy = 1.84722734378542e+03 38: Maximum force = 2.12615356182372e+04 on atom 9 38: Norm of force = 1.01988549359680e+04 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 38: 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 This run will generate roughly 0 Mb of data 38: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (235 ms) 38: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (863 ms total) 38: 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.174 0.087 199.8 38: (ns/day) (hour/ns) 38: Performance: 16.912 1.419 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.trr' 38: 38: trr version: GMX_trn_file (double precision) 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 42 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.060 0.030 199.7 38: (ns/day) (hour/ns) 38: Performance: 49.024 0.490 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (224 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 68.810 K for 38: determining the Verlet buffer size 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.212 0.106 199.8 38: (ns/day) (hour/ns) 38: Performance: 13.865 1.731 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 42 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.059 0.030 199.7 38: (ns/day) (hour/ns) 38: Performance: 49.628 0.484 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (242 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.165 0.082 199.8 38: (ns/day) (hour/ns) 38: Performance: 17.829 1.346 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 42 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.060 0.030 199.7 38: (ns/day) (hour/ns) 38: Performance: 49.252 0.487 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (240 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 1 of the 1 non-bonded parameter combinations 38: Excluding 1 bonded neighbours molecule type 'Argon' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 33.00 38: 38: There were 3 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Argon' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K 38: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.170 0.085 199.8 38: (ns/day) (hour/ns) 38: Performance: 17.307 1.387 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Argon', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 195.0 38: (ns/day) (hour/ns) 38: Performance: 1184.957 0.020 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (211 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 193.9 38: (ns/day) (hour/ns) 38: Performance: 544.174 0.044 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 194.7 38: (ns/day) (hour/ns) 38: Performance: 1126.663 0.021 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (531 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 398.997 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K 38: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 193.3 38: (ns/day) (hour/ns) 38: Performance: 590.208 0.041 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 194.3 38: (ns/day) (hour/ns) 38: Performance: 1098.929 0.022 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (530 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.002 193.0 38: (ns/day) (hour/ns) 38: Performance: 609.417 0.039 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.734 to 0.826 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.003 0.001 194.5 38: (ns/day) (hour/ns) 38: Performance: 1091.917 0.022 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (556 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 330891 of the 330891 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 330891 of the 330891 1-4 parameter combinations 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 27.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'spc2' 38: 16 steps, 0.0 ps. 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.004 0.002 192.9 38: (ns/day) (hour/ns) 38: Performance: 649.030 0.037 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.76 to 0.916 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'spc2', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 21 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.002 0.001 194.6 38: (ns/day) (hour/ns) 38: Performance: 1225.745 0.020 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (504 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.016 0.008 197.1 38: (ns/day) (hour/ns) 38: Performance: 184.168 0.130 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 24 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 196.9 38: (ns/day) (hour/ns) 38: Performance: 559.901 0.043 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (139 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 456.887 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 7 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 7 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K 38: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 53 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.021 0.011 198.0 38: (ns/day) (hour/ns) 38: Performance: 139.289 0.172 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 25 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 196.7 38: (ns/day) (hour/ns) 38: Performance: 550.446 0.044 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (136 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.020 0.010 197.4 38: (ns/day) (hour/ns) 38: Performance: 147.658 0.163 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 100, rlist from 0.745 to 0.873 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 29 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 197.0 38: (ns/day) (hour/ns) 38: Performance: 551.481 0.044 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (181 ms) 38: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp, line 28]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2145 of the 2145 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2145 of the 2145 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 38: 38: NOTE 4 [file unknown]: 38: You are using constraints on all bonds, whereas the forcefield has been 38: parametrized only with constraints involving hydrogen atoms. We suggest 38: using constraints = h-bonds instead, this will also improve performance. 38: 38: Cleaning up constraints and constant bonded interactions with virtual sites 38: Removed 18 Angles with virtual sites, 21 left 38: Removed 10 Proper Dih.s with virtual sites, 44 left 38: Converted 15 Constraints with virtual sites to connections, 7 left 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 23.00 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: There are 9 non-linear virtual site constructions. Their contribution to 38: the energy error is approximated. In most cases this does not affect the 38: error significantly. 38: 38: 38: NOTE 6 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 6 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun 'Alanine dipeptide in vacuo' 38: 16 steps, 0.0 ps. 38: turning all bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 196.6 38: (ns/day) (hour/ns) 38: Performance: 264.767 0.091 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 40, rlist from 0.727 to 0.874 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 23 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 197.1 38: (ns/day) (hour/ns) 38: Performance: 559.444 0.043 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (179 ms) 38: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (3673 ms total) 38: 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 28 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.007 196.5 38: (ns/day) (hour/ns) 38: Performance: 218.810 0.110 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.2 38: (ns/day) (hour/ns) 38: Performance: 457.628 0.052 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (146 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 196.1 38: (ns/day) (hour/ns) 38: Performance: 254.623 0.094 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 195.7 38: (ns/day) (hour/ns) 38: Performance: 447.295 0.054 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (131 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.7 38: (ns/day) (hour/ns) 38: Performance: 270.557 0.089 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.3 38: (ns/day) (hour/ns) 38: Performance: 461.468 0.052 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (148 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 54 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.021 0.011 197.7 38: (ns/day) (hour/ns) 38: Performance: 135.660 0.177 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.1 38: (ns/day) (hour/ns) 38: Performance: 474.257 0.051 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (168 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.6 38: (ns/day) (hour/ns) 38: Performance: 275.753 0.087 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 64 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 198.3 38: (ns/day) (hour/ns) 38: Performance: 212.867 0.113 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (127 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.7 38: (ns/day) (hour/ns) 38: Performance: 271.571 0.088 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.2 38: (ns/day) (hour/ns) 38: Performance: 456.645 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (141 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 54 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.021 0.011 197.6 38: (ns/day) (hour/ns) 38: Performance: 136.345 0.176 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.2 38: (ns/day) (hour/ns) 38: Performance: 453.085 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.8 38: (ns/day) (hour/ns) 38: Performance: 283.415 0.085 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 73 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.020 0.010 198.6 38: (ns/day) (hour/ns) 38: Performance: 146.312 0.164 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (151 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.5 38: (ns/day) (hour/ns) 38: Performance: 291.736 0.082 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.3 38: (ns/day) (hour/ns) 38: Performance: 454.254 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (173 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.2 38: (ns/day) (hour/ns) 38: Performance: 265.120 0.091 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.1 38: (ns/day) (hour/ns) 38: Performance: 447.035 0.054 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.5 38: (ns/day) (hour/ns) 38: Performance: 264.403 0.091 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.0 38: (ns/day) (hour/ns) 38: Performance: 474.330 0.051 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (147 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 12 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 196.2 38: (ns/day) (hour/ns) 38: Performance: 236.273 0.102 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 19 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.0 38: (ns/day) (hour/ns) 38: Performance: 453.251 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (172 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.006 196.2 38: (ns/day) (hour/ns) 38: Performance: 226.401 0.106 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.0 38: (ns/day) (hour/ns) 38: Performance: 458.275 0.052 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (144 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 11 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 196.1 38: (ns/day) (hour/ns) 38: Performance: 237.852 0.101 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.2 38: (ns/day) (hour/ns) 38: Performance: 453.085 0.053 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (124 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.8 38: (ns/day) (hour/ns) 38: Performance: 256.723 0.093 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 61 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.012 0.006 197.9 38: (ns/day) (hour/ns) 38: Performance: 241.289 0.099 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (151 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 52 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.022 0.011 197.4 38: (ns/day) (hour/ns) 38: Performance: 130.050 0.185 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.016 0.008 198.3 38: (ns/day) (hour/ns) 38: Performance: 184.350 0.130 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (126 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 196.5 38: (ns/day) (hour/ns) 38: Performance: 193.608 0.124 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 25 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.1 38: (ns/day) (hour/ns) 38: Performance: 459.095 0.052 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (144 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 196.5 38: (ns/day) (hour/ns) 38: Performance: 192.056 0.125 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 195.4 38: (ns/day) (hour/ns) 38: Performance: 493.558 0.049 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (140 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.8 38: (ns/day) (hour/ns) 38: Performance: 262.701 0.091 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 15 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 195.9 38: (ns/day) (hour/ns) 38: Performance: 527.538 0.045 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (135 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 50 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.022 0.011 197.5 38: (ns/day) (hour/ns) 38: Performance: 130.444 0.184 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 18 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.0 38: (ns/day) (hour/ns) 38: Performance: 499.036 0.048 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (152 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.7 38: (ns/day) (hour/ns) 38: Performance: 262.757 0.091 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 195.6 38: (ns/day) (hour/ns) 38: Performance: 493.914 0.049 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (152 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: NVE simulation: will use the initial temperature of 293.480 K for 38: determining the Verlet buffer size 38: 38: 38: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 5 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K 38: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 196.5 38: (ns/day) (hour/ns) 38: Performance: 194.826 0.123 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21.tpr, VERSION 2019.1 (double precision) 38: Can not increase nstlist because an NVE ensemble is used 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.016 0.008 197.9 38: (ns/day) (hour/ns) 38: Performance: 184.432 0.130 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (177 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.020 0.010 197.1 38: (ns/day) (hour/ns) 38: Performance: 146.204 0.164 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 20 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 195.6 38: (ns/day) (hour/ns) 38: Performance: 475.869 0.050 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (191 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 26 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.014 0.007 196.8 38: (ns/day) (hour/ns) 38: Performance: 209.423 0.115 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 195.4 38: (ns/day) (hour/ns) 38: Performance: 498.712 0.048 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.9 38: (ns/day) (hour/ns) 38: Performance: 267.480 0.090 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 17 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.006 0.003 196.1 38: (ns/day) (hour/ns) 38: Performance: 501.554 0.048 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (187 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.5 38: (ns/day) (hour/ns) 38: Performance: 275.149 0.087 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 67 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.015 0.008 198.2 38: (ns/day) (hour/ns) 38: Performance: 194.016 0.124 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (156 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.7 38: (ns/day) (hour/ns) 38: Performance: 268.342 0.089 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.029 0.015 199.0 38: (ns/day) (hour/ns) 38: Performance: 100.711 0.238 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (187 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.010 0.005 195.7 38: (ns/day) (hour/ns) 38: Performance: 281.203 0.085 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.013 0.007 198.0 38: (ns/day) (hour/ns) 38: Performance: 224.700 0.107 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (159 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.8 38: (ns/day) (hour/ns) 38: Performance: 261.674 0.092 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 74 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.019 0.010 198.6 38: (ns/day) (hour/ns) 38: Performance: 150.086 0.160 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (174 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.006 195.6 38: (ns/day) (hour/ns) 38: Performance: 258.664 0.093 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.008 198.5 38: (ns/day) (hour/ns) 38: Performance: 175.441 0.137 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (202 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.8 38: (ns/day) (hour/ns) 38: Performance: 269.457 0.089 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: NOTE: 16 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.005 0.003 195.6 38: (ns/day) (hour/ns) 38: Performance: 527.810 0.045 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (177 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.011 0.005 195.9 38: (ns/day) (hour/ns) 38: Performance: 273.464 0.088 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.016 0.008 198.4 38: (ns/day) (hour/ns) 38: Performance: 178.827 0.134 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (147 ms) 38: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 38: 38: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp, line 42]: 38: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 38: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 38: scheme was introduced, but the group scheme was still the default. The 38: default is now the Verlet scheme, so you will observe different behaviour. 38: 38: 38: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 38: that with the Verlet scheme, nstlist has no effect on the accuracy of 38: your simulation. 38: 38: 38: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: Setting nstcalcenergy (100) equal to nstenergy (4) 38: 38: Generated 2485 of the 2485 non-bonded parameter combinations 38: Generating 1-4 interactions: fudge = 0.5 38: Generated 2485 of the 2485 1-4 parameter combinations 38: Excluding 3 bonded neighbours molecule type 'nonanol' 38: Excluding 2 bonded neighbours molecule type 'SOL' 38: Removing all charge groups because cutoff-scheme=Verlet 38: Number of degrees of freedom in T-Coupling group System is 79.00 38: 38: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]: 38: You are using a plain Coulomb cut-off, which might produce artifacts. 38: You might want to consider using PME electrostatics. 38: 38: 38: 38: There were 4 notes 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting mdrun '30 system in water' 38: 16 steps, 0.0 ps. 38: turning H bonds into constraints... 38: turning H bonds into constraints... 38: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K 38: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm 38: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm 38: Note that mdrun will redetermine rlist based on the actual pair-list setup 38: This run will generate roughly 0 Mb of data 38: 38: Writing final coordinates. 38: 38: NOTE: 38 % of the run time was spent in pair search, 38: you might want to increase nstlist (this has no effect on accuracy) 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.009 197.2 38: (ns/day) (hour/ns) 38: Performance: 172.021 0.140 38: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32.tpr, VERSION 2019.1 (double precision) 38: Changing nstlist from 8 to 25, rlist from 0.75 to 0.883 38: 38: Using 1 MPI thread 38: Using 2 OpenMP threads 38: 38: 38: NOTE: The number of threads is not equal to the number of (logical) cores 38: and the -pin option is set to auto: will not pin threads to cores. 38: This can lead to significant performance degradation. 38: Consider using -pin on (and -pinoffset in case you run multiple jobs). 38: starting md rerun '30 system in water', reading coordinates from input trajectory '/build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.trr' 38: 38: Reading frame 0 time 0.000 Reading frame 1 time 0.004 Reading frame 2 time 0.008 Reading frame 3 time 0.012 Reading frame 4 time 0.016 Last frame 4 time 0.016 38: 38: Core t (s) Wall t (s) (%) 38: Time: 0.017 0.008 198.4 38: (ns/day) (hour/ns) 38: Performance: 174.620 0.137 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_normal.edr as double precision energy file 38: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_rerun.edr as double precision energy file 38: Reading energy frame 0 time 0.000 Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.004 Reading energy frame 1 time 0.004 Reading energy frame 2 time 0.008 Reading energy frame 2 time 0.008 Reading energy frame 3 time 0.012 Reading energy frame 3 time 0.012 Reading energy frame 4 time 0.016 Reading energy frame 4 time 0.016 Last energy frame read 4 time 0.016 Last energy frame read 4 time 0.016 38: 38: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (155 ms) 38: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (5154 ms total) 38: 38: [----------] Global test environment tear-down 38: [==========] 57 tests from 4 test cases ran. (11027 ms total) 38: [ PASSED ] 57 tests. 38/40 Test #38: MdrunNonIntegratorTests .......... Passed 11.15 sec test 39 Start 39: LegacyGroupSchemeMdrunTests 39: Test command: /build/gromacs-2019.1/build/basic-dp/bin/legacy-mdrun-test "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/LegacyGroupSchemeMdrunTests.xml" 39: Test timeout computed to be: 600 39: [==========] Running 2 tests from 1 test case. 39: [----------] Global test environment set-up. 39: [----------] 2 tests from Simple/TpiTest 39: [ RUN ] Simple/TpiTest.ReproducesOutput/0 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2019.1 (double precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 8.698e+02 8.698e+02 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/0 (469 ms) 39: [ RUN ] Simple/TpiTest.ReproducesOutput/1 39: 39: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1_input.mdp]: 39: The group cutoff scheme is deprecated since GROMACS 5.0 and will be 39: removed in a future release when all interaction forms are supported for 39: the verlet scheme. The verlet scheme already scales better, and it is 39: compatible with GPUs and other accelerators. 39: 39: Generated 331705 of the 331705 non-bonded parameter combinations 39: Generating 1-4 interactions: fudge = 0.5 39: Generated 331705 of the 331705 1-4 parameter combinations 39: Excluding 2 bonded neighbours molecule type 'SOL' 39: Excluding 3 bonded neighbours molecule type 'methane' 39: Number of degrees of freedom in T-Coupling group System is 1308.00 39: 39: There was 1 note 39: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2019.1 (double precision) 39: Using 1 MPI thread 39: 39: 39: NOTE: Thread affinity was not set. 39: 39: NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be 39: removed in a future release when 'verlet' supports all interaction forms. 39: 39: Reading frames from gro file '216 water molecules', 648 atoms. 39: Reading frame 0 time 0.000 mu 9.151e+01 9.151e+01 39: Last frame 0 time 0.000 39: Analysing residue names: 39: There are: 216 Water residues 39: There are: 1 Other residues 39: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... 39: Largest charge group radii for Van der Waals: 0.100, 0.100 nm 39: Largest charge group radii for Coulomb: 0.100, 0.100 nm 39: This run will generate roughly 0 Mb of data 39: [ OK ] Simple/TpiTest.ReproducesOutput/1 (471 ms) 39: [----------] 2 tests from Simple/TpiTest (940 ms total) 39: 39: [----------] Global test environment tear-down 39: [==========] 2 tests from 1 test case ran. (940 ms total) 39: [ PASSED ] 2 tests. 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 0.96 sec test 40 Start 40: MdrunMpiTests 40: Test command: /build/gromacs-2019.1/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "--gtest_output=xml:/build/gromacs-2019.1/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml" 40: Test timeout computed to be: 600 40: [==========] Running 21 tests from 7 test cases. 40: [----------] Global test environment set-up. 40: [----------] 1 test from DomainDecompositionSpecialCasesTest 40: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 880926019 40: Generated 3 of the 3 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 3 of the 3 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 9.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc2' 40: 0 steps, 0.0 ps. 40: 40: NOTE: 94 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.013 0.006 197.4 40: (ns/day) (hour/ns) 40: Performance: 13.575 1.768 40: This run will generate roughly 0 Mb of data 40: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (68 ms) 40: [----------] 1 test from DomainDecompositionSpecialCasesTest (68 ms total) 40: 40: [----------] 4 tests from MimicTest 40: [ RUN ] MimicTest.OneQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -2125070357 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 80 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.009 0.005 198.6 40: (ns/day) (hour/ns) 40: Performance: 18.876 1.271 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.OneQuantumMol (76 ms) 40: [ RUN ] MimicTest.AllQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 565892562 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 93 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.013 0.007 198.8 40: (ns/day) (hour/ns) 40: Performance: 12.824 1.871 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.AllQuantumMol (56 ms) 40: [ RUN ] MimicTest.TwoQuantumMol 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -647600329 40: Generated 10 of the 10 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 10 of the 10 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 21.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: NVE simulation with an initial temperature of zero: will use a Verlet 40: buffer of 10%. Check your energy drift! 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/4water.gro' 40: 40: Reading frames from gro file 'Generated by gmx solvate', 12 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 58 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 193.8 40: (ns/day) (hour/ns) 40: Performance: 82.211 0.292 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.TwoQuantumMol (52 ms) 40: [ RUN ] MimicTest.BondCuts 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp, line 3]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to -778282246 40: Generated 2211 of the 2211 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2211 of the 2211 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Protein_chain_A' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 66.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: NVE simulation: will use the initial temperature of 300.368 K for 40: determining the Verlet buffer size 40: 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/build/gromacs-2019.1/src/programs/mdrun/tests/ala.gro' 40: 40: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms. 40: Reading frame 0 time 0.000 Last frame 0 time 0.000 40: 40: NOTE: 40 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.002 0.001 194.7 40: (ns/day) (hour/ns) 40: Performance: 73.254 0.328 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K 40: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: This run will generate roughly 0 Mb of data 40: [ OK ] MimicTest.BondCuts (78 ms) 40: [----------] 4 tests from MimicTest (262 ms total) 40: 40: [----------] 1 test from MultiSimTerminationTest 40: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from MultiSimTerminationTest (0 ms total) 40: 40: [----------] 2 tests from PmeTest 40: [ RUN ] PmeTest.ReproducesEnergies 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp, line 6]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: Setting the LD random seed to 1025633931 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group rest is 12.00 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: NVE simulation: will use the initial temperature of 1046.791 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107 40: This run will generate roughly 0 Mb of data 40: 40: Writing final coordinates. 40: 40: NOTE: 15 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.096 0.048 199.7 40: (ns/day) (hour/ns) 40: Performance: 37.830 0.634 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file 40: 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/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.082 0.041 199.6 40: (ns/day) (hour/ns) 40: Performance: 44.389 0.541 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file 40: 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/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 20 steps, 0.0 ps. 40: 40: Writing final coordinates. 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.084 0.042 199.5 40: (ns/day) (hour/ns) 40: Performance: 43.059 0.557 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file 40: 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 ] PmeTest.ReproducesEnergies (279 ms) 40: [ RUN ] PmeTest.ScalesTheBox 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp, line 12]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: For a correct single-point energy evaluation with nsteps = 0, use 40: continuation = yes to avoid constraining the input coordinates. 40: 40: Setting the LD random seed to 1539160282 40: Generated 279 of the 1225 non-bonded parameter combinations 40: Excluding 2 bonded neighbours molecule type 'Methanol' 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Searching the wall atom type(s) 40: Number of degrees of freedom in T-Coupling group rest is 13.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: NVE simulation: will use the initial temperature of 966.269 K for 40: determining the Verlet buffer size 40: 40: Estimate for the relative computational load of the PME mesh part: 1.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]: 40: The optimal PME mesh load for parallel simulations is below 0.5 40: and for highly parallel simulations between 0.25 and 0.33, 40: for higher performance, increase the cut-off and the PME grid spacing. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2019.1 (double precision) 40: Can not increase nstlist because an NVE ensemble is used 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: starting mdrun 'spc-and-methanol' 40: 0 steps, 0.0 ps. 40: 40: NOTE: 41 % of the run time was spent in pair search, 40: you might want to increase nstlist (this has no effect on accuracy) 40: 40: Core t (s) Wall t (s) (%) 40: Time: 0.022 0.011 197.7 40: (ns/day) (hour/ns) 40: Performance: 7.645 3.139 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.269 K 40: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm 40: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm 40: Note that mdrun will redetermine rlist based on the actual pair-list setup 40: Calculating fourier grid dimensions for X Y Z 40: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118 40: This run will generate roughly 0 Mb of data 40: [ OK ] PmeTest.ScalesTheBox (106 ms) 40: [----------] 2 tests from PmeTest (385 ms total) 40: 40: [----------] 1 test from ReplicaExchangeTerminationTest 40: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts 40: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms) 40: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total) 40: 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -4.79910464433670e+01 40: Maximum force = 1.86297359800836e+02 on atom 13 40: Norm of force = 8.77219867200401e+01 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (401 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 330891 of the 330891 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 330891 of the 330891 1-4 parameter combinations 40: Excluding 2 bonded neighbours molecule type 'SOL' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 3.02331e+02 on atom 3 40: F-Norm = 1.18024e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -5.58622539552403e+01 40: Maximum force = 4.27274823589429e+02 on atom 13 40: Norm of force = 1.84530029788115e+02 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (391 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.19376899489616e+02 40: Maximum force = 9.99884921027275e+03 on atom 9 40: Norm of force = 4.61669565061009e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 40: 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 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (155 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: 40: NOTE 3 [file glycine_vacuo.top, line 12]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 22.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41575e+04 on atom 10 40: F-Norm = 1.18451e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.51743017875792e+02 40: Maximum force = 7.42089573427942e+03 on atom 9 40: Norm of force = 3.56929298621805e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 40: 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 turning H bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (156 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 4 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 4 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.56984194095140e+02 40: Maximum force = 4.56923625858722e+02 on atom 17 40: Norm of force = 1.83258377483269e+02 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 40: 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 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (24 ms) 40: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 2145 of the 2145 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 0.5 40: Generated 2145 of the 2145 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide' 40: 40: NOTE 3 [file unknown]: 40: You are using constraints on all bonds, whereas the forcefield has been 40: parametrized only with constraints involving hydrogen atoms. We suggest 40: using constraints = h-bonds instead, this will also improve performance. 40: 40: 40: NOTE 4 [file unknown]: 40: For accurate cg with LINCS constraints, lincs-order should be 8 or more. 40: 40: Cleaning up constraints and constant bonded interactions with virtual sites 40: Removed 18 Angles with virtual sites, 21 left 40: Removed 10 Proper Dih.s with virtual sites, 44 left 40: Converted 15 Constraints with virtual sites to connections, 7 left 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 23.00 40: 40: NOTE 5 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 5 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 1.06800e+03 on atom 28 40: F-Norm = 4.26922e+02 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = -1.69410778941233e+02 40: Maximum force = 2.18225948179418e+02 on atom 17 40: Norm of force = 7.92068036007845e+01 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 40: 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 turning all bonds into constraints... 40: This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (28 ms) 40: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (1156 ms total) 40: 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents converged to Fmax < 10 in 1 steps 40: Potential Energy = -9.74257075835447e-01 40: Maximum force = 4.01322929015133e+00 on atom 1 40: Norm of force = 1.63839399694378e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (18 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.90642313893957e-01 40: Maximum force = 2.57812909491105e+00 on atom 1 40: Norm of force = 1.05251679559258e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (12 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 1 of the 1 non-bonded parameter combinations 40: Excluding 1 bonded neighbours molecule type 'Argon' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 33.00 40: 40: There were 2 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2019.1 (double precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 4.01323e+00 on atom 1 40: F-Norm = 1.63839e+00 40: 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps 40: Potential Energy = -9.90642313893957e-01 40: Maximum force = 2.57812909491105e+00 on atom 1 40: Norm of force = 1.05251679559258e+00 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file 40: Reading energy frame 0 time 0.000 Reading energy frame 1 time 0.000 Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (14 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Steepest Descents: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Steepest Descents did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 3.19395484629892e+02 40: Maximum force = 9.97041707215792e+03 on atom 9 40: Norm of force = 4.62274878672162e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (159 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2019.1 (double precision) 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Polak-Ribiere Conjugate Gradients: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.56258793634225e+02 40: Maximum force = 7.50181017498407e+03 on atom 9 40: Norm of force = 3.61390332570590e+03 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (147 ms) 40: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 40: 40: NOTE 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp, line 28]: 40: /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it 40: was first intended for use with GROMACS before 4.6. In 4.6, the Verlet 40: scheme was introduced, but the group scheme was still the default. The 40: default is now the Verlet scheme, so you will observe different behaviour. 40: 40: 40: NOTE 2 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note 40: that with the Verlet scheme, nstlist has no effect on the accuracy of 40: your simulation. 40: 40: 40: WARNING 1 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: For efficient BFGS minimization, use switch/shift/pme instead of cut-off. 40: 40: Generated 20503 of the 20503 non-bonded parameter combinations 40: Generating 1-4 interactions: fudge = 1 40: Generated 17396 of the 20503 1-4 parameter combinations 40: Excluding 3 bonded neighbours molecule type 'Glycine' 40: Removing all charge groups because cutoff-scheme=Verlet 40: Number of degrees of freedom in T-Coupling group System is 27.00 40: 40: NOTE 3 [file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]: 40: You are using a plain Coulomb cut-off, which might produce artifacts. 40: You might want to consider using PME electrostatics. 40: 40: 40: 40: There were 3 notes 40: 40: There was 1 warning 40: Reading file /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2019.1 (double precision) 40: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank. 40: 40: Using 1 MPI thread 40: Using 2 OpenMP threads 40: 40: 40: NOTE: The number of threads is not equal to the number of (logical) cores 40: and the -pin option is set to auto: will not pin threads to cores. 40: This can lead to significant performance degradation. 40: Consider using -pin on (and -pinoffset in case you run multiple jobs). 40: 40: Low-Memory BFGS Minimizer: 40: Tolerance (Fmax) = 1.00000e+01 40: Number of steps = 4 40: Using 10 BFGS correction steps. 40: 40: F-max = 2.41672e+04 on atom 10 40: F-Norm = 1.19357e+04 40: 40: 40: Energy minimization reached the maximum number of steps before the forces 40: reached the requested precision Fmax < 10. 40: 40: writing lowest energy coordinates. 40: 40: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps. 40: Potential Energy = 1.84722734378542e+03 40: Maximum force = 2.12615356182372e+04 on atom 9 40: Norm of force = 1.01988549359680e+04 40: Opened /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file 40: 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 This run will generate roughly 0 Mb of data 40: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (144 ms) 40: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (494 ms total) 40: 40: [----------] Global test environment tear-down 40: [==========] 21 tests from 7 test cases ran. (2365 ms total) 40: [ PASSED ] 21 tests. 40: 40: YOU HAVE 4 DISABLED TESTS 40: 40/40 Test #40: MdrunMpiTests .................... Passed 2.40 sec 100% tests passed, 0 tests failed out of 40 Label Time Summary: GTest = 55.85 sec*proc (40 tests) IntegrationTest = 17.94 sec*proc (5 tests) MpiTest = 0.82 sec*proc (3 tests) SlowTest = 31.02 sec*proc (1 test) UnitTest = 6.90 sec*proc (34 tests) Total Test time (real) = 55.93 sec touch build-basic dh_testdir /usr/bin/make -j8 -C build/mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles /build/gromacs-2019.1/build/mpich/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend Scanning dependencies of target lmfit_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target tng_io_obj Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 0%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 1%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/domdec/collect.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_constraints.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_network.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_topology.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_vsite.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dump.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp 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-I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/localatomsetdata.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /build/gromacs-2019.1/src/gromacs/pbcutil/mshift.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/quadraticsplinetable.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxomp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/init.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/int64_to_int.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetree.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o 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-DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/niceheader.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/path.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp 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-DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/programcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmx_internal_xdr.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/timecontrol.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/fileio/tpxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trrio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/trxio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/warninp.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/writeps.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xdrd.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xtcio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/xvgr.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /build/gromacs-2019.1/src/gromacs/swap/swapcoords.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /build/gromacs-2019.1/src/gromacs/essentialdynamics/edsam.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/output.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/pulling/pull_rotation.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/pullutil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/bias.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/biasparams.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/correlationhistory.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /build/gromacs-2019.1/src/gromacs/imd/imdsocket.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast 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/build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/simulationsignal.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/trajectory_writing.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/update.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H 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CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/calcgrid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft5d.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/fft_fftw3.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/cpuinfo.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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/build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/md.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o 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'/build/gromacs-2019.1/build/mpich' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= Scanning dependencies of target mdrun make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src 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CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build Scanning dependencies of target tng_io_obj make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 0%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/mpich-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 1%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/viewit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/atomdistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/distribute.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlbtiming.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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/build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/basenetwork.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/compare.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/directoryenumerator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/errorcodes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/exceptions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fatalerror.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/sysinfo.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/matio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/pdbio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/shellfc.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/shellfc.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-grid.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-load-balancing.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-load-balancing.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-only.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-only.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-redistribute.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-redistribute.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-solve.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-solve.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spline-work.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spline-work.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-spread.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-spread.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/gromacs/gpu_utils/clfftinitializer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/identifyavx512fmaunits.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/integrator.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/integrator.cpp cd 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/build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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/build/gromacs-2019.1/src/gromacs/taskassignment/findallgputasks.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/reportgpuusage.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/resourcedivision.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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dependencies of target mdrun make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/mdrun.dir/mdrun_main.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -o ../../bin/mdrun_mpi_d.mpich -Wl,-rpath,:::::::::::::::::::::::::::::::: ../../lib/libgromacs_mdrun_mpi_d.mpich.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lpthread -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 0 make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' sed -e 's/#MPIABBR#/mpich/g' -e 's/#MPIPROG#/MPICH/g' \ < debian/gromacs-parallel.README.Debian.in \ > debian/gromacs-mpich.README.Debian /usr/bin/make -j8 -C build/mpich tests make[1]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles 99 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich 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/build/gromacs-2019.1/build/mpich/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build Scanning dependencies of target gmock [ 2%] Built target tng_io_obj [ 3%] Built target libgromacs_external make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' Scanning dependencies of target onlinehelp-test-shared /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/gromacs-2019.1/build/mpich/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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 [ 4%] Built target lmfit_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp /usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 22%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 79%] Built target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 79%] Built target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 80%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/mpich/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/mpich/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 81%] 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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/testutils /build/gromacs-2019.1/build/mpich/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 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CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H 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-DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/mpich/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o 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/build/gromacs-2019.1/build/mpich/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/testutils/tests /build/gromacs-2019.1/build/mpich/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target testutils-mpi-test Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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 Scanning dependencies of target applied-forces-test make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build Scanning dependencies of target domdec-test Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 83%] Built target testutils-mpi-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp [ 84%] Built target compat-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests /build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 84%] Built target listed-forces-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 84%] Built target 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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests /build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 84%] Built target domdec-test cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 85%] Built target fft-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 85%] Built target hardware-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/libgromacs_mdrun_mpi.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 86%] Built target testutils-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 86%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 86%] Built target mdrunutility-mpi-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 87%] Built target onlinehelp-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests /build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 87%] Built target gpu_utils-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests /build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 88%] Built target restraintpotential-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 89%] Built target mdlib-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 90%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= [ 91%] Built target taskassignment-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 92%] Built target commandline-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 93%] 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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests /build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 93%] Built target table-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 93%] Built target pull-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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 93%] Built target fileio-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 94%] Built target random-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 94%] Built target math-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 94%] Built target awh-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 96%] Built target simd-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp [ 97%] Built target options-test cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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_mdrun_mpi.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich' (cd build/mpich; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/mpich/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/mpich/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/mpich/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/mpich/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/mpich/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/mpich 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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/mpich/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (6 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (0 ms) 1: [----------] 34 tests from ReferenceDataTest (16 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (3 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (25 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 0.08 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "/build/gromacs-2019.1/build/mpich/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (0 ms total) 2: [ PASSED ] 1 test. 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.05 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/mpich/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (1 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (1 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (4 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 0.06 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/mpich/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (1 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.04 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/mpich/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (1 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (1 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (2 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (2 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 0.04 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/mpich/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (5 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (1 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms) 6: [----------] 13 tests from CommandLineParserTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (1 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (5 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (18 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.05 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/mpich/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (0 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.03 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/mpich/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (4 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (5 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (7 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (7 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (51 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (0 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (70 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (25 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (8 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (13 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (22 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (25 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (29 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (84 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (370 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 0.45 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/mpich/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (8 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (12 ms) 9: [----------] 2 tests from ManyFFTTest (22 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 9: [----------] 1 test from FFTTest (9 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (3 ms) 9: [----------] 1 test from FFFTest3D (3 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (7 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (11 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (30 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (65 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.10 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/mpich/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (3 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.05 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/mpich/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (21 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (22 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (24 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (22 ms) 11: [----------] 4 tests from HardwareTopologyTest (89 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (89 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 0.12 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/mpich/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (0 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (0 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (1 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (1 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (1 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (0 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 12: [----------] 21 tests from FunctionTest (4 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (1 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (6 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (13 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.05 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/mpich/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (5 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (11 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (11 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.04 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.mpich "-np" "4" "/build/gromacs-2019.1/build/mpich/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (2 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (4 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (6 ms total) 14: [ PASSED ] 13 tests. 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.08 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/mpich/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (5 ms) 15: [----------] 3 tests from HelpManagerTest (5 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (0 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (2 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (8 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.04 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/mpich/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (5 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (6 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (1 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (1 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (1 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms) 16: [----------] 8 tests from TreeValueSupportTest (3 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (15 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.05 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/mpich/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (0 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (0 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (1 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (4 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (11 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 0.06 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/mpich/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.03 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/mpich/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (1 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (34 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (65 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (70 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (16 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (64 ms) 19: [----------] 10 tests from SplineTableTest/0 (260 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (1 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (5 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (10 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (11 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (3 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (10 ms) 19: [----------] 10 tests from SplineTableTest/1 (50 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (310 ms total) 19: [ PASSED ] 20 tests. 19/27 Test #19: TableUnitTests ................... Passed 0.34 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/mpich/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.03 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/mpich/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (0 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (6 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (1 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (1 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (1 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (0 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (2 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (1 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (3 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (1 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (1 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (1 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (1 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (26 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.08 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.mpich "-np" "4" "/build/gromacs-2019.1/build/mpich/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (1 ms total) 22: [ PASSED ] 2 tests. 22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.05 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/mpich/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (2 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (2 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (3 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (5 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (8 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 0.04 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/mpich/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (0 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.03 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/mpich/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (2 ms) 25: [----------] 1 test from gridTest (2 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (9 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.04 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/mpich/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 277 tests from 22 test cases. 26: [----------] Global test environment set-up. 26: [----------] 9 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadStore 26: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadU 26: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4StoreU 26: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 26: [----------] 9 tests from SimdBootstrapTest (0 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 26: 26: [----------] 16 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (1 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 26: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 26: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 26: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 26: [----------] 16 tests from SimdFloatingpointUtilTest (1 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (0 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (1 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (0 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (0 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (1 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (2 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (2 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (4 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (1 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (2 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (2 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (2 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (9 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (0 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (1 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (6 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (8 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (3 ms) 26: [----------] 45 tests from SimdMathTest (72 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (1 ms total) 26: 26: [----------] 32 tests from Simd4FloatingpointTest 26: [ RUN ] Simd4FloatingpointTest.setZero 26: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 26: [ RUN ] Simd4FloatingpointTest.set 26: [ OK ] Simd4FloatingpointTest.set (0 ms) 26: [ RUN ] Simd4FloatingpointTest.add 26: [ OK ] Simd4FloatingpointTest.add (0 ms) 26: [ RUN ] Simd4FloatingpointTest.sub 26: [ OK ] Simd4FloatingpointTest.sub (0 ms) 26: [ RUN ] Simd4FloatingpointTest.mul 26: [ OK ] Simd4FloatingpointTest.mul (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fma 26: [ OK ] Simd4FloatingpointTest.fma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fms 26: [ OK ] Simd4FloatingpointTest.fms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnma 26: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnms 26: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.abs 26: [ OK ] Simd4FloatingpointTest.abs (0 ms) 26: [ RUN ] Simd4FloatingpointTest.neg 26: [ OK ] Simd4FloatingpointTest.neg (0 ms) 26: [ RUN ] Simd4FloatingpointTest.and 26: [ OK ] Simd4FloatingpointTest.and (0 ms) 26: [ RUN ] Simd4FloatingpointTest.or 26: [ OK ] Simd4FloatingpointTest.or (0 ms) 26: [ RUN ] Simd4FloatingpointTest.xor 26: [ OK ] Simd4FloatingpointTest.xor (0 ms) 26: [ RUN ] Simd4FloatingpointTest.andNot 26: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 26: [ RUN ] Simd4FloatingpointTest.max 26: [ OK ] Simd4FloatingpointTest.max (0 ms) 26: [ RUN ] Simd4FloatingpointTest.min 26: [ OK ] Simd4FloatingpointTest.min (0 ms) 26: [ RUN ] Simd4FloatingpointTest.round 26: [ OK ] Simd4FloatingpointTest.round (0 ms) 26: [ RUN ] Simd4FloatingpointTest.trunc 26: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 26: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 26: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.selectByNotMask 26: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpNe 26: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLe 26: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLt 26: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 26: [ RUN ] Simd4FloatingpointTest.andB 26: [ OK ] Simd4FloatingpointTest.andB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.orB 26: [ OK ] Simd4FloatingpointTest.orB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.anyTrue 26: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 26: [ RUN ] Simd4FloatingpointTest.blend 26: [ OK ] Simd4FloatingpointTest.blend (0 ms) 26: [ RUN ] Simd4FloatingpointTest.reduce 26: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 26: [ RUN ] Simd4FloatingpointTest.dotProduct 26: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 26: [ RUN ] Simd4FloatingpointTest.transpose 26: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 26: [----------] 32 tests from Simd4FloatingpointTest (1 ms total) 26: 26: [----------] 1 test from Simd4VectorOperationsTest 26: [ RUN ] Simd4VectorOperationsTest.norm2 26: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 26: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 26: 26: [----------] 2 tests from Simd4MathTest 26: [ RUN ] Simd4MathTest.invsqrt 26: [ OK ] Simd4MathTest.invsqrt (0 ms) 26: [ RUN ] Simd4MathTest.invsqrtSingleaccuracy 26: [ OK ] Simd4MathTest.invsqrtSingleaccuracy (1 ms) 26: [----------] 2 tests from Simd4MathTest (1 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (0 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (1 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 277 tests from 22 test cases ran. (78 ms total) 26: [ PASSED ] 277 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.12 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/mpich/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.03 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 2.21 sec*proc (27 tests) MpiTest = 0.19 sec*proc (3 tests) UnitTest = 2.21 sec*proc (27 tests) Total Test time (real) = 2.26 sec /usr/bin/make -j8 -C build/mpich-dp tests make[1]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 99 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/external/googletest /build/gromacs-2019.1/build/mpich-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= /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]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 1%] Built target lmfit_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build Scanning dependencies of target gmock make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 3%] Built target tng_io_obj /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc cd /build/gromacs-2019.1/build/mpich-dp/src/external/googletest && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build Scanning dependencies of target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build [ 4%] Built target libgromacs_external Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 22%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 79%] Built target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 79%] Built target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 80%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/mpich-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/mpich-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 81%] 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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/testutils /build/gromacs-2019.1/build/mpich-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/mpich-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 83%] Built target testutils /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test Scanning dependencies of target testutils-mpi-test Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp Scanning dependencies of target applied-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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 Scanning dependencies of target testutils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' Scanning dependencies of target commandline-test /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp Scanning dependencies of target mdlib-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 83%] Built target testutils-mpi-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 [ 84%] Built target compat-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 84%] Built target listed-forces-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 84%] Built target applied-forces-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 84%] 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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp /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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 85%] Built target fft-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 85%] Built target hardware-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/libgromacs_mdrun_mpi_d.mpich.a ../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 86%] Built target testutils-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 86%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 86%] Built target mdrunutility-mpi-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 86%] Built target gpu_utils-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 87%] 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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 88%] 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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 89%] Built target mdlib-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 90%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 91%] Built target taskassignment-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 92%] Built target commandline-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 92%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 93%] Built target ewald-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 93%] Built target table-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 93%] Built target fileio-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 93%] Built target math-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 94%] Built target random-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 94%] Built target awh-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 96%] Built target simd-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 97%] Built target options-test cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/mpich-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/mpich-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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_mdrun_mpi_d.mpich.a ../../../../lib/libgmock.a -lpthread -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm -lpthread make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' (cd build/mpich-dp ; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/mpich-dp/lib ctest -V || dpkg-architecture -i hurd-i386 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/mpich-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/mpich-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/mpich-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/mpich-dp/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/mpich-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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (5 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (0 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (10 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (15 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (1 ms) 1: [----------] 4 tests from XvgTests (3 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (29 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 0.06 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.mpich "-np" "2" "/build/gromacs-2019.1/build/mpich-dp/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (1 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (1 ms total) 2: [ PASSED ] 1 test. 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.07 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (5 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (5 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (1 ms) 3: [----------] 7 tests from SignalTest (1 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (0 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (1 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (8 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 0.05 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (0 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (5 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (5 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (5 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.04 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (1 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (1 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (2 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (2 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 0.05 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (5 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (7 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (2 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (1 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (18 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.05 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (1 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.04 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (4 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (5 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (10 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (1 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (66 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (82 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (30 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (10 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (18 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (28 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (27 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (4 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (4 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (33 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (90 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (447 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 0.53 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (6 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (18 ms) 9: [----------] 2 tests from ManyFFTTest (25 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 9: [----------] 1 test from FFTTest (4 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (3 ms) 9: [----------] 1 test from FFFTest3D (3 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (6 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (23 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (55 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.10 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (1 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (3 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.04 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (25 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (26 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (24 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (23 ms) 11: [----------] 4 tests from HardwareTopologyTest (99 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (99 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 0.13 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (0 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (1 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (0 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (1 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (1 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms) 12: [----------] 21 tests from FunctionTest (4 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (6 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.05 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (5 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (0 ms) 13: [----------] 17 tests from ThreadAffinityTest (10 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (10 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.05 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.mpich "-np" "4" "/build/gromacs-2019.1/build/mpich-dp/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (1 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (3 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (1 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (4 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (7 ms total) 14: [ PASSED ] 13 tests. 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.07 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (0 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (2 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (4 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.05 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (1 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (9 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (9 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (1 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (1 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (1 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (19 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.06 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (1 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (1 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (0 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (0 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (11 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (11 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (1 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (2 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (16 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 0.07 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (1 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.03 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (2 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (41 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (68 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (74 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (17 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (67 ms) 19: [----------] 10 tests from SplineTableTest/0 (277 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (3 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (90 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (175 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (182 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (41 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (165 ms) 19: [----------] 10 tests from SplineTableTest/1 (666 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (943 ms total) 19: [ PASSED ] 20 tests. 19/27 Test #19: TableUnitTests ................... Passed 0.98 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.03 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (0 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (1 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (6 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (1 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (4 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (4 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (0 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (0 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (0 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (1 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (1 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms) 21: [----------] 7 tests from StringUtilityTest (1 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (1 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (1 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (2 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (3 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (29 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.08 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.mpich "-np" "4" "/build/gromacs-2019.1/build/mpich-dp/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (0 ms total) 22: [ PASSED ] 2 tests. 22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.07 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (2 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (2 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (3 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (6 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (8 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 0.04 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (1 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (1 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (1 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.04 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (0 ms) 25: [----------] 1 test from BiasTest (0 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (1 ms) 25: [----------] 1 test from gridTest (1 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (8 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.04 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: [==========] Running 236 tests from 19 test cases. 26: [----------] Global test environment set-up. 26: [----------] 6 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [----------] 6 tests from SimdBootstrapTest (1 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 26: 26: [----------] 13 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [----------] 13 tests from SimdFloatingpointUtilTest (1 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (1 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (7 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (1 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (1 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (2 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (3 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (2 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (3 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (2 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (2 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (2 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (3 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (3 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (12 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (2 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (1 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (0 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (6 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (2 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (4 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (3 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (7 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (5 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (3 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (2 ms) 26: [----------] 45 tests from SimdMathTest (104 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (1 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (2 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 236 tests from 19 test cases ran. (110 ms total) 26: [ PASSED ] 236 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.15 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/mpich-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/mpich-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.03 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 3.00 sec*proc (27 tests) MpiTest = 0.21 sec*proc (3 tests) UnitTest = 3.00 sec*proc (27 tests) Total Test time (real) = 3.05 sec touch build-mpich dh_testdir /usr/bin/make -j8 -C build/openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles /build/gromacs-2019.1/build/openmpi/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= Scanning dependencies of target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 0%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 1%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/openmpi/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/pargs.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/shellcompletions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/cellsizes.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_setup.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/domdec_specatomcomm.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/ga2la.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/compare.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/fileredirector.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/gmxomp.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/init.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/inmemoryserializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/int64_to_int.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetree.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/logger.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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-isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/pleasecite.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/programcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && 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-isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/strconvert.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fileio/gmxfio-xdr.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/gmxfio-xdr.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/ns.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/ns.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_orca.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/long-range-correction.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/long-range-correction.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gpu-program-impl.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gpu-program-impl.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/parallel_3dfft.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/gpu_utils.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 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/build/gromacs-2019.1/src/gromacs/mdrun/minimize.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/multisim.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/multisim.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/rerun.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/mimic.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/runner.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/tpi.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/handlerestart.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/mdmodules.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/mdmodules.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-fexcess-precision=fast -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target tng_io_obj make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c Scanning dependencies of target mdrun_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build Scanning dependencies of target libgromacs_external make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/programs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c Scanning dependencies of target libgromacs_generated make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/warnmalloc.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/widemuldiv.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 0%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicc.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/openmpi-dp/tng/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 1%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/errhandler.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/tmpi_malloc.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/atomic.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/atomic.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/system_error.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/system_error.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJEw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEwSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJEw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/openmpi-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineinit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/filenm.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/box.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/dlb.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/rstparser.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /build/gromacs-2019.1/src/gromacs/topology/symtab.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/ikeyvaluetreeerror.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/niceheader.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/boxdeformation.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/forcerec.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong 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/build/gromacs-2019.1/src/gromacs/mdlib/groupcoord.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/lincs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/md_support.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdatoms.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdebin_bar.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdoutf.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/mdsetup.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/mdsetup.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/membed.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_atomdata.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_atomdata.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_cpu.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nsgrid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/perf_est.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gamess.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_gaussian.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qm_mopac.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 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CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/qmmm.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rbin.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/resethandler.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/rf_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/calculate-spline-moduli.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/calculate-spline-moduli.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-gather.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-gather.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/ewald/pme-pp.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/pme-pp.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g 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-I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/legacymdrunoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/logging.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/logging.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/replicaexchange.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrun/simulationcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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-DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/threadaffinity.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractoption.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/abstractsection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/basicoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/behaviorcollection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoption.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/options.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsassigner.cpp cd 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-I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/optionsvisitor.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 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CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/openmpi-dp/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -fopenmp -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/manager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DHAVE_CONFIG_H 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src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= /usr/bin/make -f 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Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests 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src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build [ 1%] Built target lmfit_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Scanning dependencies of target mdrunutility-test-shared Scanning dependencies of target gmock [ 2%] Built target libgromacs_external make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Scanning dependencies of target onlinehelp-test-shared /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]: Leaving 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CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 22%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 79%] Built target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 79%] Built target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 80%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 81%] 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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils /build/gromacs-2019.1/build/openmpi/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 83%] Built target testutils /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils/tests /build/gromacs-2019.1/build/openmpi/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/testutils/tests /build/gromacs-2019.1/build/openmpi/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target compat-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp Scanning dependencies of target testutils-test Scanning dependencies of target mdlib-test Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Scanning dependencies of target applied-forces-test Scanning dependencies of target domdec-test /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Scanning dependencies of target testutils-mpi-test /usr/bin/make -f src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build.make src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp /usr/bin/make -f src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build.make src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 83%] Built target testutils-mpi-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] Built target compat-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] Built target listed-forces-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] Built target 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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 84%] 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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 85%] Built target fft-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 85%] Built target hardware-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp cd /build/gromacs-2019.1/build/openmpi/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/libgromacs_mdrun_mpi.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 86%] Built target testutils-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 86%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 86%] Built target mdrunutility-mpi-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 86%] Built target gpu_utils-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 87%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 88%] Built target restraintpotential-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 89%] Built target mdlib-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 90%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 91%] Built target taskassignment-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 92%] Built target commandline-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 92%] Built target pull-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target ewald-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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target table-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target fileio-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target math-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 93%] Built target awh-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 94%] Built target random-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 95%] Built target options-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 97%] Built target simd-test cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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_mdrun_mpi.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libhwloc.so -lrt /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi' (cd build/openmpi ; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/openmpi/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/openmpi 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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/openmpi/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: -------------------------------------------------------------------------- 1: [[23842,1],0]: A high-performance Open MPI point-to-point messaging module 1: was unable to find any relevant network interfaces: 1: 1: Module: OpenFabrics (openib) 1: Host: codethink13-arm64 1: 1: Another transport will be used instead, although this may result in 1: lower performance. 1: 1: NOTE: You can disable this warning by setting the MCA parameter 1: btl_base_warn_component_unused to 0. 1: -------------------------------------------------------------------------- 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (6 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (12 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (0 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (1 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (3 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (21 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 0.29 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "/build/gromacs-2019.1/build/openmpi/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: -------------------------------------------------------------------------- 2: [[23867,1],1]: A high-performance Open MPI point-to-point messaging module 2: was unable to find any relevant network interfaces: 2: 2: Module: OpenFabrics (openib) 2: Host: codethink13-arm64 2: 2: Another transport will be used instead, although this may result in 2: lower performance. 2: 2: NOTE: You can disable this warning by setting the MCA parameter 2: btl_base_warn_component_unused to 0. 2: -------------------------------------------------------------------------- 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (0 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (0 ms total) 2: [ PASSED ] 1 test. 2: [codethink13-arm64:31666] 1 more process has sent help message help-mpi-btl-base.txt / btl:no-nics 2: [codethink13-arm64:31666] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.41 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/openmpi/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: -------------------------------------------------------------------------- 3: [[23881,1],0]: A high-performance Open MPI point-to-point messaging module 3: was unable to find any relevant network interfaces: 3: 3: Module: OpenFabrics (openib) 3: Host: codethink13-arm64 3: 3: Another transport will be used instead, although this may result in 3: lower performance. 3: 3: NOTE: You can disable this warning by setting the MCA parameter 3: btl_base_warn_component_unused to 0. 3: -------------------------------------------------------------------------- 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (1 ms) 3: [----------] 1 test from VerletBufferConstraintTest (1 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (0 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (1 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (1 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (0 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (4 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 0.25 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/openmpi/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: -------------------------------------------------------------------------- 4: [[23873,1],0]: A high-performance Open MPI point-to-point messaging module 4: was unable to find any relevant network interfaces: 4: 4: Module: OpenFabrics (openib) 4: Host: codethink13-arm64 4: 4: Another transport will be used instead, although this may result in 4: lower performance. 4: 4: NOTE: You can disable this warning by setting the MCA parameter 4: btl_base_warn_component_unused to 0. 4: -------------------------------------------------------------------------- 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (1 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (1 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (1 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.27 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/openmpi/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: -------------------------------------------------------------------------- 5: [[23899,1],0]: A high-performance Open MPI point-to-point messaging module 5: was unable to find any relevant network interfaces: 5: 5: Module: OpenFabrics (openib) 5: Host: codethink13-arm64 5: 5: Another transport will be used instead, although this may result in 5: lower performance. 5: 5: NOTE: You can disable this warning by setting the MCA parameter 5: btl_base_warn_component_unused to 0. 5: -------------------------------------------------------------------------- 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (1 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (2 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (2 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 0.25 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/openmpi/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: -------------------------------------------------------------------------- 6: [[23890,1],0]: A high-performance Open MPI point-to-point messaging module 6: was unable to find any relevant network interfaces: 6: 6: Module: OpenFabrics (openib) 6: Host: codethink13-arm64 6: 6: Another transport will be used instead, although this may result in 6: lower performance. 6: 6: NOTE: You can disable this warning by setting the MCA parameter 6: btl_base_warn_component_unused to 0. 6: -------------------------------------------------------------------------- 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (1 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (0 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (1 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (4 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (12 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.30 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/openmpi/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: -------------------------------------------------------------------------- 7: [[23914,1],0]: A high-performance Open MPI point-to-point messaging module 7: was unable to find any relevant network interfaces: 7: 7: Module: OpenFabrics (openib) 7: Host: codethink13-arm64 7: 7: Another transport will be used instead, although this may result in 7: lower performance. 7: 7: NOTE: You can disable this warning by setting the MCA parameter 7: btl_base_warn_component_unused to 0. 7: -------------------------------------------------------------------------- 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (0 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (0 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.29 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/openmpi/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: -------------------------------------------------------------------------- 8: [[23909,1],0]: A high-performance Open MPI point-to-point messaging module 8: was unable to find any relevant network interfaces: 8: 8: Module: OpenFabrics (openib) 8: Host: codethink13-arm64 8: 8: Another transport will be used instead, although this may result in 8: lower performance. 8: 8: NOTE: You can disable this warning by setting the MCA parameter 8: btl_base_warn_component_unused to 0. 8: -------------------------------------------------------------------------- 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (3 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (5 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (5 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (58 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (5 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (0 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (75 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (25 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (9 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (13 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (1 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (22 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (25 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (3 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (28 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (87 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (434 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 0.76 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/openmpi/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: -------------------------------------------------------------------------- 9: [[23927,1],0]: A high-performance Open MPI point-to-point messaging module 9: was unable to find any relevant network interfaces: 9: 9: Module: OpenFabrics (openib) 9: Host: codethink13-arm64 9: 9: Another transport will be used instead, although this may result in 9: lower performance. 9: 9: NOTE: You can disable this warning by setting the MCA parameter 9: btl_base_warn_component_unused to 0. 9: -------------------------------------------------------------------------- 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (9 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (14 ms) 9: [----------] 2 tests from ManyFFTTest (24 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (9 ms) 9: [----------] 1 test from FFTTest (10 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (3 ms) 9: [----------] 1 test from FFFTest3D (4 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (3 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (12 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (16 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (40 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (78 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.36 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/openmpi/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: -------------------------------------------------------------------------- 10: [[23182,1],0]: A high-performance Open MPI point-to-point messaging module 10: was unable to find any relevant network interfaces: 10: 10: Module: OpenFabrics (openib) 10: Host: codethink13-arm64 10: 10: Another transport will be used instead, although this may result in 10: lower performance. 10: 10: NOTE: You can disable this warning by setting the MCA parameter 10: btl_base_warn_component_unused to 0. 10: -------------------------------------------------------------------------- 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (1 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (1 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (0 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (2 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.26 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/openmpi/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: -------------------------------------------------------------------------- 11: [[23195,1],0]: A high-performance Open MPI point-to-point messaging module 11: was unable to find any relevant network interfaces: 11: 11: Module: OpenFabrics (openib) 11: Host: codethink13-arm64 11: 11: Another transport will be used instead, although this may result in 11: lower performance. 11: 11: NOTE: You can disable this warning by setting the MCA parameter 11: btl_base_warn_component_unused to 0. 11: -------------------------------------------------------------------------- 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (29 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (28 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (28 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (29 ms) 11: [----------] 4 tests from HardwareTopologyTest (114 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (114 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 0.40 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/openmpi/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: -------------------------------------------------------------------------- 12: [[23188,1],0]: A high-performance Open MPI point-to-point messaging module 12: was unable to find any relevant network interfaces: 12: 12: Module: OpenFabrics (openib) 12: Host: codethink13-arm64 12: 12: Another transport will be used instead, although this may result in 12: lower performance. 12: 12: NOTE: You can disable this warning by setting the MCA parameter 12: btl_base_warn_component_unused to 0. 12: -------------------------------------------------------------------------- 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (1 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (0 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (0 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (0 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (1 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 12: [----------] 21 tests from FunctionTest (4 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (1 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (6 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.33 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/openmpi/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: -------------------------------------------------------------------------- 13: [[23215,1],0]: A high-performance Open MPI point-to-point messaging module 13: was unable to find any relevant network interfaces: 13: 13: Module: OpenFabrics (openib) 13: Host: codethink13-arm64 13: 13: Another transport will be used instead, although this may result in 13: lower performance. 13: 13: NOTE: You can disable this warning by setting the MCA parameter 13: btl_base_warn_component_unused to 0. 13: -------------------------------------------------------------------------- 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (7 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (7 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.30 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: -------------------------------------------------------------------------- 14: [[23206,1],0]: A high-performance Open MPI point-to-point messaging module 14: was unable to find any relevant network interfaces: 14: 14: Module: OpenFabrics (openib) 14: Host: codethink13-arm64 14: 14: Another transport will be used instead, although this may result in 14: lower performance. 14: 14: NOTE: You can disable this warning by setting the MCA parameter 14: btl_base_warn_component_unused to 0. 14: -------------------------------------------------------------------------- 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (76 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (57 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (73 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (61 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (65 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (65 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (488 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (25 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (0 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (519 ms total) 14: [ PASSED ] 13 tests. 14: [codethink13-arm64:31791] 3 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics 14: [codethink13-arm64:31791] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 1.08 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/openmpi/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: -------------------------------------------------------------------------- 15: [[23240,1],0]: A high-performance Open MPI point-to-point messaging module 15: was unable to find any relevant network interfaces: 15: 15: Module: OpenFabrics (openib) 15: Host: codethink13-arm64 15: 15: Another transport will be used instead, although this may result in 15: lower performance. 15: 15: NOTE: You can disable this warning by setting the MCA parameter 15: btl_base_warn_component_unused to 0. 15: -------------------------------------------------------------------------- 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (0 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (2 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (4 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.27 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/openmpi/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: -------------------------------------------------------------------------- 16: [[23232,1],0]: A high-performance Open MPI point-to-point messaging module 16: was unable to find any relevant network interfaces: 16: 16: Module: OpenFabrics (openib) 16: Host: codethink13-arm64 16: 16: Another transport will be used instead, although this may result in 16: lower performance. 16: 16: NOTE: You can disable this warning by setting the MCA parameter 16: btl_base_warn_component_unused to 0. 16: -------------------------------------------------------------------------- 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (1 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (1 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (1 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (1 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms) 16: [----------] 9 tests from OptionsAssignerTest (2 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (1 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (1 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (1 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (0 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (2 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (2 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (1 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (13 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.22 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/openmpi/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: -------------------------------------------------------------------------- 17: [[23256,1],0]: A high-performance Open MPI point-to-point messaging module 17: was unable to find any relevant network interfaces: 17: 17: Module: OpenFabrics (openib) 17: Host: codethink13-arm64 17: 17: Another transport will be used instead, although this may result in 17: lower performance. 17: 17: NOTE: You can disable this warning by setting the MCA parameter 17: btl_base_warn_component_unused to 0. 17: -------------------------------------------------------------------------- 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (0 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (0 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (0 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (0 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (0 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (2 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (2 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (1 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (0 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (8 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 0.27 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/openmpi/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: -------------------------------------------------------------------------- 18: [[23248,1],0]: A high-performance Open MPI point-to-point messaging module 18: was unable to find any relevant network interfaces: 18: 18: Module: OpenFabrics (openib) 18: Host: codethink13-arm64 18: 18: Another transport will be used instead, although this may result in 18: lower performance. 18: 18: NOTE: You can disable this warning by setting the MCA parameter 18: btl_base_warn_component_unused to 0. 18: -------------------------------------------------------------------------- 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.29 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/openmpi/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: -------------------------------------------------------------------------- 19: [[23272,1],0]: A high-performance Open MPI point-to-point messaging module 19: was unable to find any relevant network interfaces: 19: 19: Module: OpenFabrics (openib) 19: Host: codethink13-arm64 19: 19: Another transport will be used instead, although this may result in 19: lower performance. 19: 19: NOTE: You can disable this warning by setting the MCA parameter 19: btl_base_warn_component_unused to 0. 19: -------------------------------------------------------------------------- 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (1 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (34 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (65 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (71 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (16 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (64 ms) 19: [----------] 10 tests from SplineTableTest/0 (259 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (1 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (5 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (3 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (0 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (11 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (11 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (3 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (11 ms) 19: [----------] 10 tests from SplineTableTest/1 (51 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (311 ms total) 19: [ PASSED ] 20 tests. 19/27 Test #19: TableUnitTests ................... Passed 0.52 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/openmpi/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: -------------------------------------------------------------------------- 20: [[23264,1],0]: A high-performance Open MPI point-to-point messaging module 20: was unable to find any relevant network interfaces: 20: 20: Module: OpenFabrics (openib) 20: Host: codethink13-arm64 20: 20: Another transport will be used instead, although this may result in 20: lower performance. 20: 20: NOTE: You can disable this warning by setting the MCA parameter 20: btl_base_warn_component_unused to 0. 20: -------------------------------------------------------------------------- 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (1 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (1 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.27 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/openmpi/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: -------------------------------------------------------------------------- 21: [[23288,1],0]: A high-performance Open MPI point-to-point messaging module 21: was unable to find any relevant network interfaces: 21: 21: Module: OpenFabrics (openib) 21: Host: codethink13-arm64 21: 21: Another transport will be used instead, although this may result in 21: lower performance. 21: 21: NOTE: You can disable this warning by setting the MCA parameter 21: btl_base_warn_component_unused to 0. 21: -------------------------------------------------------------------------- 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (1 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (0 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (0 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (1 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (0 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (1 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (0 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (0 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (9 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (10 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 21: [----------] 7 tests from StringUtilityTest (0 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (1 ms) 21: [----------] 2 tests from FormatStringTest (1 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (0 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (0 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (4 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (4 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (9 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (1 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (1 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (31 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.33 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: -------------------------------------------------------------------------- 22: [[23049,1],1]: A high-performance Open MPI point-to-point messaging module 22: was unable to find any relevant network interfaces: 22: 22: Module: OpenFabrics (openib) 22: Host: codethink13-arm64 22: 22: Another transport will be used instead, although this may result in 22: lower performance. 22: 22: NOTE: You can disable this warning by setting the MCA parameter 22: btl_base_warn_component_unused to 0. 22: -------------------------------------------------------------------------- 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (54 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (88 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (170 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (170 ms total) 22: [ PASSED ] 2 tests. 22: [codethink13-arm64:31872] 3 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics 22: [codethink13-arm64:31872] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.74 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/openmpi/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: -------------------------------------------------------------------------- 23: [[23067,1],0]: A high-performance Open MPI point-to-point messaging module 23: was unable to find any relevant network interfaces: 23: 23: Module: OpenFabrics (openib) 23: Host: codethink13-arm64 23: 23: Another transport will be used instead, although this may result in 23: lower performance. 23: 23: NOTE: You can disable this warning by setting the MCA parameter 23: btl_base_warn_component_unused to 0. 23: -------------------------------------------------------------------------- 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (1 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (0 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (5 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (7 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 0.28 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/openmpi/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: -------------------------------------------------------------------------- 24: [[23059,1],0]: A high-performance Open MPI point-to-point messaging module 24: was unable to find any relevant network interfaces: 24: 24: Module: OpenFabrics (openib) 24: Host: codethink13-arm64 24: 24: Another transport will be used instead, although this may result in 24: lower performance. 24: 24: NOTE: You can disable this warning by setting the MCA parameter 24: btl_base_warn_component_unused to 0. 24: -------------------------------------------------------------------------- 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (0 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.30 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/openmpi/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: -------------------------------------------------------------------------- 25: [[23083,1],0]: A high-performance Open MPI point-to-point messaging module 25: was unable to find any relevant network interfaces: 25: 25: Module: OpenFabrics (openib) 25: Host: codethink13-arm64 25: 25: Another transport will be used instead, although this may result in 25: lower performance. 25: 25: NOTE: You can disable this warning by setting the MCA parameter 25: btl_base_warn_component_unused to 0. 25: -------------------------------------------------------------------------- 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (1 ms) 25: [----------] 1 test from gridTest (1 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (6 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (9 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.26 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/openmpi/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: -------------------------------------------------------------------------- 26: [[23075,1],0]: A high-performance Open MPI point-to-point messaging module 26: was unable to find any relevant network interfaces: 26: 26: Module: OpenFabrics (openib) 26: Host: codethink13-arm64 26: 26: Another transport will be used instead, although this may result in 26: lower performance. 26: 26: NOTE: You can disable this warning by setting the MCA parameter 26: btl_base_warn_component_unused to 0. 26: -------------------------------------------------------------------------- 26: [==========] Running 277 tests from 22 test cases. 26: [----------] Global test environment set-up. 26: [----------] 9 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadStore 26: [ OK ] SimdBootstrapTest.simd4LoadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4LoadU 26: [ OK ] SimdBootstrapTest.simd4LoadU (0 ms) 26: [ RUN ] SimdBootstrapTest.simd4StoreU 26: [ OK ] SimdBootstrapTest.simd4StoreU (0 ms) 26: [----------] 9 tests from SimdBootstrapTest (0 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (1 ms total) 26: 26: [----------] 16 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadUNDuplicate4 26: [ OK ] SimdFloatingpointUtilTest.loadUNDuplicate4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.load4DuplicateN 26: [ OK ] SimdFloatingpointUtilTest.load4DuplicateN (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.loadU4NOffset 26: [ OK ] SimdFloatingpointUtilTest.loadU4NOffset (0 ms) 26: [----------] 16 tests from SimdFloatingpointUtilTest (0 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (1 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (1 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (0 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (0 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (0 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (2 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (1 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (2 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (1 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (2 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (1 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (2 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (13 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (0 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (0 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (6 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (8 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (2 ms) 26: [----------] 45 tests from SimdMathTest (69 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (1 ms total) 26: 26: [----------] 32 tests from Simd4FloatingpointTest 26: [ RUN ] Simd4FloatingpointTest.setZero 26: [ OK ] Simd4FloatingpointTest.setZero (0 ms) 26: [ RUN ] Simd4FloatingpointTest.set 26: [ OK ] Simd4FloatingpointTest.set (0 ms) 26: [ RUN ] Simd4FloatingpointTest.add 26: [ OK ] Simd4FloatingpointTest.add (0 ms) 26: [ RUN ] Simd4FloatingpointTest.sub 26: [ OK ] Simd4FloatingpointTest.sub (0 ms) 26: [ RUN ] Simd4FloatingpointTest.mul 26: [ OK ] Simd4FloatingpointTest.mul (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fma 26: [ OK ] Simd4FloatingpointTest.fma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fms 26: [ OK ] Simd4FloatingpointTest.fms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnma 26: [ OK ] Simd4FloatingpointTest.fnma (0 ms) 26: [ RUN ] Simd4FloatingpointTest.fnms 26: [ OK ] Simd4FloatingpointTest.fnms (0 ms) 26: [ RUN ] Simd4FloatingpointTest.abs 26: [ OK ] Simd4FloatingpointTest.abs (0 ms) 26: [ RUN ] Simd4FloatingpointTest.neg 26: [ OK ] Simd4FloatingpointTest.neg (0 ms) 26: [ RUN ] Simd4FloatingpointTest.and 26: [ OK ] Simd4FloatingpointTest.and (0 ms) 26: [ RUN ] Simd4FloatingpointTest.or 26: [ OK ] Simd4FloatingpointTest.or (0 ms) 26: [ RUN ] Simd4FloatingpointTest.xor 26: [ OK ] Simd4FloatingpointTest.xor (0 ms) 26: [ RUN ] Simd4FloatingpointTest.andNot 26: [ OK ] Simd4FloatingpointTest.andNot (0 ms) 26: [ RUN ] Simd4FloatingpointTest.max 26: [ OK ] Simd4FloatingpointTest.max (0 ms) 26: [ RUN ] Simd4FloatingpointTest.min 26: [ OK ] Simd4FloatingpointTest.min (0 ms) 26: [ RUN ] Simd4FloatingpointTest.round 26: [ OK ] Simd4FloatingpointTest.round (0 ms) 26: [ RUN ] Simd4FloatingpointTest.trunc 26: [ OK ] Simd4FloatingpointTest.trunc (0 ms) 26: [ RUN ] Simd4FloatingpointTest.gmxSimd4RsqrtR 26: [ OK ] Simd4FloatingpointTest.gmxSimd4RsqrtR (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] Simd4FloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.selectByNotMask 26: [ OK ] Simd4FloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpNe 26: [ OK ] Simd4FloatingpointTest.cmpNe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLe 26: [ OK ] Simd4FloatingpointTest.cmpLe (0 ms) 26: [ RUN ] Simd4FloatingpointTest.cmpLt 26: [ OK ] Simd4FloatingpointTest.cmpLt (0 ms) 26: [ RUN ] Simd4FloatingpointTest.andB 26: [ OK ] Simd4FloatingpointTest.andB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.orB 26: [ OK ] Simd4FloatingpointTest.orB (0 ms) 26: [ RUN ] Simd4FloatingpointTest.anyTrue 26: [ OK ] Simd4FloatingpointTest.anyTrue (0 ms) 26: [ RUN ] Simd4FloatingpointTest.blend 26: [ OK ] Simd4FloatingpointTest.blend (0 ms) 26: [ RUN ] Simd4FloatingpointTest.reduce 26: [ OK ] Simd4FloatingpointTest.reduce (0 ms) 26: [ RUN ] Simd4FloatingpointTest.dotProduct 26: [ OK ] Simd4FloatingpointTest.dotProduct (0 ms) 26: [ RUN ] Simd4FloatingpointTest.transpose 26: [ OK ] Simd4FloatingpointTest.transpose (0 ms) 26: [----------] 32 tests from Simd4FloatingpointTest (0 ms total) 26: 26: [----------] 1 test from Simd4VectorOperationsTest 26: [ RUN ] Simd4VectorOperationsTest.norm2 26: [ OK ] Simd4VectorOperationsTest.norm2 (0 ms) 26: [----------] 1 test from Simd4VectorOperationsTest (0 ms total) 26: 26: [----------] 2 tests from Simd4MathTest 26: [ RUN ] Simd4MathTest.invsqrt 26: [ OK ] Simd4MathTest.invsqrt (1 ms) 26: [ RUN ] Simd4MathTest.invsqrtSingleaccuracy 26: [ OK ] Simd4MathTest.invsqrtSingleaccuracy (0 ms) 26: [----------] 2 tests from Simd4MathTest (1 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (1 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (0 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 277 tests from 22 test cases ran. (73 ms total) 26: [ PASSED ] 277 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.35 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/openmpi/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: -------------------------------------------------------------------------- 27: [[23099,1],0]: A high-performance Open MPI point-to-point messaging module 27: was unable to find any relevant network interfaces: 27: 27: Module: OpenFabrics (openib) 27: Host: codethink13-arm64 27: 27: Another transport will be used instead, although this may result in 27: lower performance. 27: 27: NOTE: You can disable this warning by setting the MCA parameter 27: btl_base_warn_component_unused to 0. 27: -------------------------------------------------------------------------- 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (0 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (0 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.27 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 9.92 sec*proc (27 tests) MpiTest = 2.23 sec*proc (3 tests) UnitTest = 9.92 sec*proc (27 tests) Total Test time (real) = 10.32 sec /usr/bin/make -j8 -C build/openmpi-dp tests make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 tests make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 99 /usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/external/googletest /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest/CMakeFiles/gmock.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' Scanning dependencies of target gmock make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/external/googletest/CMakeFiles/gmock.dir/build.make src/external/googletest/CMakeFiles/gmock.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build Scanning dependencies of target onlinehelp-test-shared make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googlemock/src/gmock-all.cc make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -D_GNU_SOURCE=1 -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googlemock -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/googletest/googletest -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wno-unused-variable -o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o -c /build/gromacs-2019.1/src/external/googletest/googletest/src/gtest-all.cc make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build [ 1%] Built target lmfit_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/mock_helptopic.cpp [ 2%] Built target libgromacs_external Scanning dependencies of target mdrunutility-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp [ 4%] Built target tng_io_obj make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 22%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 79%] Built target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 79%] Built target onlinehelp-test-shared make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 80%] Built target mdrunutility-test-shared cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -P CMakeFiles/gmock.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/external/googletest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1 /usr/bin/ar qc ../../../lib/libgmock.a CMakeFiles/gmock.dir/googlemock/src/gmock-all.cc.o CMakeFiles/gmock.dir/googletest/src/gtest-all.cc.o /usr/bin/ranlib ../../../lib/libgmock.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 81%] 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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils /build/gromacs-2019.1/build/openmpi-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color= Scanning dependencies of target testutils make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /build/gromacs-2019.1/src/testutils/cmdlinetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/conftest.cpp.o -c /build/gromacs-2019.1/src/testutils/conftest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /build/gromacs-2019.1/src/testutils/filematchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/interactivetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /build/gromacs-2019.1/src/testutils/loggertest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpi-printer.cpp.o -c /build/gromacs-2019.1/src/testutils/mpi-printer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/mpitest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/refdata-xml.cpp.o -c /build/gromacs-2019.1/src/testutils/refdata-xml.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /build/gromacs-2019.1/src/testutils/stdiohelper.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /build/gromacs-2019.1/src/testutils/stringtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /build/gromacs-2019.1/src/testutils/testasserts.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /build/gromacs-2019.1/src/testutils/testfilemanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /build/gromacs-2019.1/src/testutils/testfileredirector.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testinit.cpp.o -c /build/gromacs-2019.1/src/testutils/testinit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/testmatchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /build/gromacs-2019.1/src/testutils/testoptions.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /build/gromacs-2019.1/src/testutils/textblockmatchers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /build/gromacs-2019.1/src/testutils/xvgtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /build/gromacs-2019.1/src/external/tinyxml2/tinyxml2.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1 /usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi-printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata-xml.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o /usr/bin/ranlib ../../lib/libtestutils.a make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 83%] Built target testutils /usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend /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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/CMakeFiles/applied-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/CMakeFiles/listed-forces-test.dir/DependInfo.cmake --color= /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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color= Scanning dependencies of target testutils-mpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/mpitest.cpp Scanning dependencies of target compat-test Scanning dependencies of target domdec-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/hashedmap.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/make_unique.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/make_unique.cpp Scanning dependencies of target applied-forces-test Scanning dependencies of target listed-forces-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' Scanning dependencies of target mdlib-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/build make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' Scanning dependencies of target testutils-test /usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/electricfield.cpp.o -c /build/gromacs-2019.1/src/gromacs/applied-forces/tests/electricfield.cpp /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]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/calc_verletbuf.cpp /usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/bonded.cpp.o -c /build/gromacs-2019.1/src/gromacs/listed-forces/tests/bonded.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/interactivetest.cpp Scanning dependencies of target commandline-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /build/gromacs-2019.1/src/gromacs/compat/tests/pointers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/listed-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/mdebin.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/mdebin.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 83%] Built target testutils-mpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color= Scanning dependencies of target ewald-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmebsplinetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/refdata_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/listed-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/listed-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/listed-forces-test.dir/bonded.cpp.o CMakeFiles/listed-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/listed-forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/domdec/tests/localatomsetmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/compat-test.dir/make_unique.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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied-forces/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/applied-forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/settle.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] Built target compat-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color= Scanning dependencies of target fft-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/fft.cpp.o -c /build/gromacs-2019.1/src/gromacs/fft/tests/fft.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/applied-forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied-forces-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] Built target listed-forces-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color= Scanning dependencies of target gpu_utils-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/gputest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] Built target 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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color= Scanning dependencies of target hardware-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /build/gromacs-2019.1/src/gromacs/hardware/tests/hardwaretopology.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/hostallocator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 84%] 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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color= Scanning dependencies of target math-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/arrayrefwithpadding.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmegathertest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/testasserts_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 85%] Built target fft-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/shake.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 85%] Built target hardware-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target mdrunutility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdrunutility/tests/threadaffinity-mpi.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /build/gromacs-2019.1/src/testutils/tests/xvgtest_tests.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/dofit.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/dofit.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/testutils/../external/tinyxml2 -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/libgromacs_mdrun_mpi_d.openmpi.a ../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/functions.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/functions.cpp [ 86%] Built target testutils-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color= Scanning dependencies of target onlinehelp-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpformat.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/simulationsignal.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpmanager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 86%] Built target mdrunutility-test /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color= Scanning dependencies of target options-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/abstractoptionstorage.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesolvetest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity-mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 86%] Built target mdrunutility-mpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color= Scanning dependencies of target random-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/exponentialdistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroups.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/invertmatrix.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/onlinehelp/tests/helpwritercontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineparser.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /build/gromacs-2019.1/src/gromacs/gpu_utils/tests/devicetransfers.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/gammadistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/paddedvector.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/tests/updategroupscog.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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 CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 86%] Built target gpu_utils-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color= Scanning dependencies of target restraintpotential-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /build/gromacs-2019.1/src/gromacs/restraint/tests/manager.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 87%] Built target onlinehelp-test /usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color= Scanning dependencies of target table-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /build/gromacs-2019.1/src/gromacs/tables/tests/splinetable.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmesplinespreadtest.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/mdebin.cpp.o CMakeFiles/mdlib-test.dir/settle.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/normaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoption.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 88%] Built target restraintpotential-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color= Scanning dependencies of target taskassignment-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /build/gromacs-2019.1/src/gromacs/taskassignment/tests/usergpuids.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 89%] Built target mdlib-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color= Scanning dependencies of target utility-mpi-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator-mpi.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator-mpi.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/tests/pargs.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/seed.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/seed.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 90%] Built target utility-mpi-test /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/filenameoptionmanager.cpp Scanning dependencies of target utility-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/alignedallocator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/tabulatednormaldistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/pmetestcommon.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 91%] Built target taskassignment-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color= Scanning dependencies of target fileio-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/confio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 92%] Built target commandline-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /build/gromacs-2019.1/src/gromacs/ewald/tests/testhardwarecontexts.cpp Scanning dependencies of target pull-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/pull.cpp.o -c /build/gromacs-2019.1/src/gromacs/pulling/tests/pull.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/threefry.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/threefry.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/filemd5.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/option.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/option.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/arrayref.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /build/gromacs-2019.1/src/gromacs/math/tests/vectypes.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target ewald-test /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/readinp.cpp Scanning dependencies of target awh-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/bias.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/bias.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/optionsassigner.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target pull-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color= Scanning dependencies of target simd-test make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/bootstrap_loadstore.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target table-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/repeatingsection.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/base.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/base.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /build/gromacs-2019.1/src/gromacs/fileio/tests/tngio.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformintdistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/invertmatrix.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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target fileio-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 93%] Built target math-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_floatingpoint_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/biasstate.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /build/gromacs-2019.1/src/gromacs/random/tests/uniformrealdistribution.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/timeunitmanager.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /build/gromacs-2019.1/src/gromacs/options/tests/treesupport.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/grid.cpp.o -c /build/gromacs-2019.1/src/gromacs/awh/tests/grid.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_math.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_memory.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd_integer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 94%] Built target random-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask32.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 94%] Built target awh-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask64.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_floatingpoint.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 95%] Built target options-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/bitmask128.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_vector_operations.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/simd4_math.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreeserializer.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/keyvaluetreetransform.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_util.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /build/gromacs-2019.1/src/gromacs/simd/tests/scalar_math.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/gmxregex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/gmxregex.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/logger.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/logger.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/mutex.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/path.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/path.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/physicalnodecommunicator.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/stringutil.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textreader.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/textwriter.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /build/gromacs-2019.1/src/gromacs/utility/tests/typetraits.cpp cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.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_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.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/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/mpicxx.openmpi -DGMX_DOUBLE=1 -DGTEST_HAS_PTHREAD=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/build/gromacs-2019.1/build/openmpi-dp/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/googletest/googletest/include -isystem /build/gromacs-2019.1/src/external/googletest/googlemock/include -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /build/gromacs-2019.1/src/testutils/unittest_main.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 97%] Built target simd-test cd /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1 /usr/bin/mpicxx.openmpi -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now -Wl,--as-needed 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/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/gmxregex.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.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_mdrun_mpi_d.openmpi.a ../../../../lib/libgmock.a -fopenmp /usr/lib/aarch64-linux-gnu/libz.so /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 /usr/lib/aarch64-linux-gnu/liblapack.so -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target utility-test /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1 /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles/tests.dir/DependInfo.cmake --color= Scanning dependencies of target tests make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target tests make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' (cd build/openmpi-dp ; LD_LIBRARY_PATH=/build/gromacs-2019.1/build/openmpi-dp/lib \ OMPI_MCA_plm_rsh_agent=/bin/false \ OMPI_MCA_rmaps_base_oversubscribe=1 \ ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 ) UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl UpdateCTestConfiguration from :/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Parse Config file:/build/gromacs-2019.1/build/openmpi-dp/DartConfiguration.tcl Test project /build/gromacs-2019.1/build/openmpi-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: TestUtilsUnitTests 1: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/testutils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TestUtilsUnitTests.xml" 1: Test timeout computed to be: 30 1: -------------------------------------------------------------------------- 1: [[30010,1],0]: A high-performance Open MPI point-to-point messaging module 1: was unable to find any relevant network interfaces: 1: 1: Module: OpenFabrics (openib) 1: Host: codethink13-arm64 1: 1: Another transport will be used instead, although this may result in 1: lower performance. 1: 1: NOTE: You can disable this warning by setting the MCA parameter 1: btl_base_warn_component_unused to 0. 1: -------------------------------------------------------------------------- 1: [==========] Running 59 tests from 5 test cases. 1: [----------] Global test environment set-up. 1: [----------] 10 tests from InteractiveTestHelperTest 1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession 1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (1 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput 1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput 1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (0 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput 1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (1 ms) 1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput 1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (1 ms) 1: [----------] 10 tests from InteractiveTestHelperTest (7 ms total) 1: 1: [----------] 34 tests from ReferenceDataTest 1: [ RUN ] ReferenceDataTest.HandlesSimpleData 1: [ OK ] ReferenceDataTest.HandlesSimpleData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData 1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks 1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringBlockData 1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVectorData 1: [ OK ] ReferenceDataTest.HandlesVectorData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceData 1: [ OK ] ReferenceDataTest.HandlesSequenceData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData 1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectData 1: [ OK ] ReferenceDataTest.HandlesIncorrectData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType 1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingData 1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedData 1: [ OK ] ReferenceDataTest.HandlesUncheckedData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound 1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariants 1: [ OK ] ReferenceDataTest.HandlesVariants (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree 1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey 1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectValue 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectValue (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesVariantsWithIncorrectType 1: [ OK ] ReferenceDataTest.HandlesVariantsWithIncorrectType (5 ms) 1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile 1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings 1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace 1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings 1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock 1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices 1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData 1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds 1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesReadingValues 1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (0 ms) 1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries 1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms) 1: [----------] 34 tests from ReferenceDataTest (17 ms total) 1: 1: [----------] 7 tests from FloatingPointDifferenceTest 1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues 1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues 1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign 1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero 1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero 1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms) 1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN 1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms) 1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total) 1: 1: [----------] 4 tests from FloatingPointToleranceTest 1: [ RUN ] FloatingPointToleranceTest.UlpTolerance 1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms) 1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp 1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms) 1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance 1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms) 1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total) 1: 1: [----------] 4 tests from XvgTests 1: [ RUN ] XvgTests.CreateFile 1: [ OK ] XvgTests.CreateFile (1 ms) 1: [ RUN ] XvgTests.CheckMissing 1: [ OK ] XvgTests.CheckMissing (1 ms) 1: [ RUN ] XvgTests.CheckExtra 1: [ OK ] XvgTests.CheckExtra (0 ms) 1: [ RUN ] XvgTests.ReadIncorrect 1: [ OK ] XvgTests.ReadIncorrect (0 ms) 1: [----------] 4 tests from XvgTests (3 ms total) 1: 1: [----------] Global test environment tear-down 1: [==========] 59 tests from 5 test cases ran. (27 ms total) 1: [ PASSED ] 59 tests. 1/27 Test #1: TestUtilsUnitTests ............... Passed 0.31 sec test 2 Start 2: TestUtilsMpiUnitTests 2: Test command: /usr/bin/mpiexec.openmpi "-np" "2" "/build/gromacs-2019.1/build/openmpi-dp/bin/testutils-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml" 2: Test timeout computed to be: 30 2: -------------------------------------------------------------------------- 2: [[30023,1],0]: A high-performance Open MPI point-to-point messaging module 2: was unable to find any relevant network interfaces: 2: 2: Module: OpenFabrics (openib) 2: Host: codethink13-arm64 2: 2: Another transport will be used instead, although this may result in 2: lower performance. 2: 2: NOTE: You can disable this warning by setting the MCA parameter 2: btl_base_warn_component_unused to 0. 2: -------------------------------------------------------------------------- 2: [==========] Running 1 test from 1 test case. 2: [----------] Global test environment set-up. 2: [----------] 1 test from MpiSelfTest 2: [ RUN ] MpiSelfTest.Runs 2: [ OK ] MpiSelfTest.Runs (0 ms) 2: [----------] 1 test from MpiSelfTest (1 ms total) 2: 2: [----------] Global test environment tear-down 2: [==========] 1 test from 1 test case ran. (1 ms total) 2: [ PASSED ] 1 test. 2: [codethink13-arm64:21454] 1 more process has sent help message help-mpi-btl-base.txt / btl:no-nics 2: [codethink13-arm64:21454] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 2/27 Test #2: TestUtilsMpiUnitTests ............ Passed 0.34 sec test 3 Start 3: MdlibUnitTest 3: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/mdlib-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdlibUnitTest.xml" 3: Test timeout computed to be: 30 3: -------------------------------------------------------------------------- 3: [[30074,1],0]: A high-performance Open MPI point-to-point messaging module 3: was unable to find any relevant network interfaces: 3: 3: Module: OpenFabrics (openib) 3: Host: codethink13-arm64 3: 3: Another transport will be used instead, although this may result in 3: lower performance. 3: 3: NOTE: You can disable this warning by setting the MCA parameter 3: btl_base_warn_component_unused to 0. 3: -------------------------------------------------------------------------- 3: [==========] Running 50 tests from 8 test cases. 3: [----------] Global test environment set-up. 3: [----------] 1 test from VerletBufferConstraintTest 3: [ RUN ] VerletBufferConstraintTest.EqualMasses 3: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms) 3: [----------] 1 test from VerletBufferConstraintTest (0 ms total) 3: 3: [----------] 3 tests from PrintEbin 3: [ RUN ] PrintEbin.print_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.print_ebin_HandlesEmptyAverages (0 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesAverages (1 ms) 3: [ RUN ] PrintEbin.pr_ebin_HandlesEmptyAverages 3: [ OK ] PrintEbin.pr_ebin_HandlesEmptyAverages (0 ms) 3: [----------] 3 tests from PrintEbin (1 ms total) 3: 3: [----------] 4 tests from ShakeTest 3: [ RUN ] ShakeTest.ConstrainsOneBond 3: [ OK ] ShakeTest.ConstrainsOneBond (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds 3: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms) 3: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom 3: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms) 3: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms 3: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms) 3: [----------] 4 tests from ShakeTest (0 ms total) 3: 3: [----------] 1 test from NullSignalTest 3: [ RUN ] NullSignalTest.NullSignallerWorks 3: [ OK ] NullSignalTest.NullSignallerWorks (0 ms) 3: [----------] 1 test from NullSignalTest (0 ms total) 3: 3: [----------] 7 tests from SignalTest 3: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace 3: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms) 3: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms) 3: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace 3: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms) 3: [----------] 7 tests from SignalTest (0 ms total) 3: 3: [----------] 9 tests from UpdateGroups 3: [ RUN ] UpdateGroups.ethaneUA 3: [ OK ] UpdateGroups.ethaneUA (0 ms) 3: [ RUN ] UpdateGroups.methane 3: [ OK ] UpdateGroups.methane (0 ms) 3: [ RUN ] UpdateGroups.ethane 3: [ OK ] UpdateGroups.ethane (0 ms) 3: [ RUN ] UpdateGroups.butaneUA 3: [ OK ] UpdateGroups.butaneUA (0 ms) 3: [ RUN ] UpdateGroups.waterThreeSite 3: [ OK ] UpdateGroups.waterThreeSite (0 ms) 3: [ RUN ] UpdateGroups.waterFourSite 3: [ OK ] UpdateGroups.waterFourSite (0 ms) 3: [ RUN ] UpdateGroups.fourAtomsWithSettle 3: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms) 3: [ RUN ] UpdateGroups.waterFlexAngle 3: [ OK ] UpdateGroups.waterFlexAngle (0 ms) 3: [ RUN ] UpdateGroups.twoMoltypes 3: [ OK ] UpdateGroups.twoMoltypes (0 ms) 3: [----------] 9 tests from UpdateGroups (1 ms total) 3: 3: [----------] 1 test from UpdateGroupsCog 3: [ RUN ] UpdateGroupsCog.ComputesCogs 3: [ OK ] UpdateGroupsCog.ComputesCogs (1 ms) 3: [----------] 1 test from UpdateGroupsCog (1 ms total) 3: 3: [----------] 24 tests from WithParameters/SettleTest 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/13 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/13 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/14 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/14 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/15 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/15 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/16 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/16 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/17 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/17 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/18 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/18 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/19 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/19 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/20 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/20 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/21 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/21 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/22 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/22 (0 ms) 3: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/23 3: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/23 (0 ms) 3: [----------] 24 tests from WithParameters/SettleTest (1 ms total) 3: 3: [----------] Global test environment tear-down 3: [==========] 50 tests from 8 test cases ran. (4 ms total) 3: [ PASSED ] 50 tests. 3/27 Test #3: MdlibUnitTest .................... Passed 0.30 sec test 4 Start 4: AppliedForcesUnitTest 4: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/applied-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/AppliedForcesUnitTest.xml" 4: Test timeout computed to be: 30 4: -------------------------------------------------------------------------- 4: [[29328,1],0]: A high-performance Open MPI point-to-point messaging module 4: was unable to find any relevant network interfaces: 4: 4: Module: OpenFabrics (openib) 4: Host: codethink13-arm64 4: 4: Another transport will be used instead, although this may result in 4: lower performance. 4: 4: NOTE: You can disable this warning by setting the MCA parameter 4: btl_base_warn_component_unused to 0. 4: -------------------------------------------------------------------------- 4: [==========] Running 3 tests from 1 test case. 4: [----------] Global test environment set-up. 4: [----------] 3 tests from ElectricFieldTest 4: [ RUN ] ElectricFieldTest.Static 4: [ OK ] ElectricFieldTest.Static (0 ms) 4: [ RUN ] ElectricFieldTest.Oscillating 4: [ OK ] ElectricFieldTest.Oscillating (0 ms) 4: [ RUN ] ElectricFieldTest.Pulsed 4: [ OK ] ElectricFieldTest.Pulsed (0 ms) 4: [----------] 3 tests from ElectricFieldTest (0 ms total) 4: 4: [----------] Global test environment tear-down 4: [==========] 3 tests from 1 test case ran. (0 ms total) 4: [ PASSED ] 3 tests. 4/27 Test #4: AppliedForcesUnitTest ............ Passed 0.26 sec test 5 Start 5: ListedForcesTest 5: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/listed-forces-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/ListedForcesTest.xml" 5: Test timeout computed to be: 30 5: -------------------------------------------------------------------------- 5: [[29369,1],0]: A high-performance Open MPI point-to-point messaging module 5: was unable to find any relevant network interfaces: 5: 5: Module: OpenFabrics (openib) 5: Host: codethink13-arm64 5: 5: Another transport will be used instead, although this may result in 5: lower performance. 5: 5: NOTE: You can disable this warning by setting the MCA parameter 5: btl_base_warn_component_unused to 0. 5: -------------------------------------------------------------------------- 5: [==========] Running 15 tests from 1 test case. 5: [----------] Global test environment set-up. 5: [----------] 15 tests from BondedTest 5: [ RUN ] BondedTest.BondAnglePbcNone 5: [ OK ] BondedTest.BondAnglePbcNone (1 ms) 5: [ RUN ] BondedTest.BondAnglePbcXy 5: [ OK ] BondedTest.BondAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.BondAnglePbcXyz 5: [ OK ] BondedTest.BondAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcNone 5: [ OK ] BondedTest.DihedralAnglePbcNone (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXy 5: [ OK ] BondedTest.DihedralAnglePbcXy (0 ms) 5: [ RUN ] BondedTest.DihedralAnglePbcXyz 5: [ OK ] BondedTest.DihedralAnglePbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcNo 5: [ OK ] BondedTest.IfuncBondsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXy 5: [ OK ] BondedTest.IfuncBondsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncBondsPbcXyz 5: [ OK ] BondedTest.IfuncBondsPbcXyz (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcNo 5: [ OK ] BondedTest.IfuncAnglesPbcNo (1 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXy 5: [ OK ] BondedTest.IfuncAnglesPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncAnglesPbcXYZ 5: [ OK ] BondedTest.IfuncAnglesPbcXYZ (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcNo 5: [ OK ] BondedTest.IfuncProperDihedralsPbcNo (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXy 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXy (0 ms) 5: [ RUN ] BondedTest.IfuncProperDihedralsPbcXyz 5: [ OK ] BondedTest.IfuncProperDihedralsPbcXyz (0 ms) 5: [----------] 15 tests from BondedTest (2 ms total) 5: 5: [----------] Global test environment tear-down 5: [==========] 15 tests from 1 test case ran. (2 ms total) 5: [ PASSED ] 15 tests. 5/27 Test #5: ListedForcesTest ................. Passed 0.27 sec test 6 Start 6: CommandLineUnitTests 6: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/commandline-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/CommandLineUnitTests.xml" 6: Test timeout computed to be: 30 6: -------------------------------------------------------------------------- 6: [[29390,1],0]: A high-performance Open MPI point-to-point messaging module 6: was unable to find any relevant network interfaces: 6: 6: Module: OpenFabrics (openib) 6: Host: codethink13-arm64 6: 6: Another transport will be used instead, although this may result in 6: lower performance. 6: 6: NOTE: You can disable this warning by setting the MCA parameter 6: btl_base_warn_component_unused to 0. 6: -------------------------------------------------------------------------- 6: [==========] Running 55 tests from 6 test cases. 6: [----------] Global test environment set-up. 6: [----------] 3 tests from CommandLineHelpModuleTest 6: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp 6: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (1 ms) 6: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic 6: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (0 ms) 6: [ RUN ] CommandLineHelpModuleTest.ExportsHelp 6: [ OK ] CommandLineHelpModuleTest.ExportsHelp (2 ms) 6: [----------] 3 tests from CommandLineHelpModuleTest (3 ms total) 6: 6: [----------] 6 tests from CommandLineHelpWriterTest 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables 6: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions 6: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (0 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups 6: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms) 6: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText 6: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (0 ms) 6: [----------] 6 tests from CommandLineHelpWriterTest (2 ms total) 6: 6: [----------] 6 tests from CommandLineModuleManagerTest 6: [ RUN ] CommandLineModuleManagerTest.RunsModule 6: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule 6: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (0 ms) 6: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames 6: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms) 6: [----------] 6 tests from CommandLineModuleManagerTest (1 ms total) 6: 6: [----------] 13 tests from CommandLineParserTest 6: [ RUN ] CommandLineParserTest.HandlesSingleValues 6: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument 6: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms) 6: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument 6: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms) 6: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers 6: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesString 6: [ OK ] CommandLineParserTest.HandlesString (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues 6: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix 6: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers 6: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms) 6: [ RUN ] CommandLineParserTest.HandlesSkipUnknown 6: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms) 6: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault 6: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms) 6: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments 6: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms) 6: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions 6: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms) 6: [----------] 13 tests from CommandLineParserTest (1 ms total) 6: 6: [----------] 6 tests from CommandLineProgramContextTest 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (1 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms) 6: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink 6: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms) 6: [----------] 6 tests from CommandLineProgramContextTest (1 ms total) 6: 6: [----------] 21 tests from ParseCommonArgsTest 6: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs 6: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesInt64Args 6: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesRealArgs 6: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesStringArgs 6: [ OK ] ParseCommonArgsTest.ParsesStringArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs 6: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs 6: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit 6: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs 6: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgs 6: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms) 6: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (1 ms) 6: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension 6: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles 6: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (0 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified 6: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (0 ms) 6: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles 6: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (5 ms) 6: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension 6: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (0 ms) 6: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName 6: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (0 ms) 6: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs 6: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (0 ms) 6: [----------] 21 tests from ParseCommonArgsTest (7 ms total) 6: 6: [----------] Global test environment tear-down 6: [==========] 55 tests from 6 test cases ran. (15 ms total) 6: [ PASSED ] 55 tests. 6/27 Test #6: CommandLineUnitTests ............. Passed 0.26 sec test 7 Start 7: DomDecTests 7: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/domdec-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/DomDecTests.xml" 7: Test timeout computed to be: 30 7: -------------------------------------------------------------------------- 7: [[29399,1],0]: A high-performance Open MPI point-to-point messaging module 7: was unable to find any relevant network interfaces: 7: 7: Module: OpenFabrics (openib) 7: Host: codethink13-arm64 7: 7: Another transport will be used instead, although this may result in 7: lower performance. 7: 7: NOTE: You can disable this warning by setting the MCA parameter 7: btl_base_warn_component_unused to 0. 7: -------------------------------------------------------------------------- 7: [==========] Running 9 tests from 2 test cases. 7: [----------] Global test environment set-up. 7: [----------] 7 tests from HashedMap 7: [ RUN ] HashedMap.InsertsFinds 7: [ OK ] HashedMap.InsertsFinds (0 ms) 7: [ RUN ] HashedMap.NegativeKeysWork 7: [ OK ] HashedMap.NegativeKeysWork (0 ms) 7: [ RUN ] HashedMap.InsertsErases 7: [ OK ] HashedMap.InsertsErases (0 ms) 7: [ RUN ] HashedMap.InsertsOrAssigns 7: [ OK ] HashedMap.InsertsOrAssigns (0 ms) 7: [ RUN ] HashedMap.Clears 7: [ OK ] HashedMap.Clears (0 ms) 7: [ RUN ] HashedMap.LinkedEntries 7: [ OK ] HashedMap.LinkedEntries (0 ms) 7: [ RUN ] HashedMap.ResizesTable 7: [ OK ] HashedMap.ResizesTable (0 ms) 7: [----------] 7 tests from HashedMap (1 ms total) 7: 7: [----------] 2 tests from LocalAtomSetManager 7: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet 7: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms) 7: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices 7: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms) 7: [----------] 2 tests from LocalAtomSetManager (0 ms total) 7: 7: [----------] Global test environment tear-down 7: [==========] 9 tests from 2 test cases ran. (1 ms total) 7: [ PASSED ] 9 tests. 7/27 Test #7: DomDecTests ...................... Passed 0.28 sec test 8 Start 8: EwaldUnitTests 8: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/ewald-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/EwaldUnitTests.xml" 8: Test timeout computed to be: 30 8: -------------------------------------------------------------------------- 8: [[29436,1],0]: A high-performance Open MPI point-to-point messaging module 8: was unable to find any relevant network interfaces: 8: 8: Module: OpenFabrics (openib) 8: Host: codethink13-arm64 8: 8: Another transport will be used instead, although this may result in 8: lower performance. 8: 8: NOTE: You can disable this warning by setting the MCA parameter 8: btl_base_warn_component_unused to 0. 8: -------------------------------------------------------------------------- 8: [==========] Running 257 tests from 10 test cases. 8: [----------] Global test environment set-up. 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (4 ms) 8: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 8: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (0 ms) 8: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (4 ms total) 8: 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (8 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (6 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (6 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (1 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (2 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (3 ms) 8: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 8: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (2 ms) 8: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (65 ms total) 8: 8: [----------] 144 tests from SaneInput/PmeGatherTest 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (1 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (0 ms) 8: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143 8: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (1 ms) 8: [----------] 144 tests from SaneInput/PmeGatherTest (77 ms total) 8: 8: [----------] 16 tests from SaneInput/PmeSolveTest 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (3 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (2 ms) 8: [----------] 16 tests from SaneInput/PmeSolveTest (30 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (2 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (10 ms total) 8: 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (2 ms) 8: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (18 ms total) 8: 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (3 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (0 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (2 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (1 ms) 8: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 8: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (2 ms) 8: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (27 ms total) 8: 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (1 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (2 ms) 8: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (2 ms) 8: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (25 ms total) 8: 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (1 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (2 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (3 ms) 8: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (4 ms) 8: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (29 ms total) 8: 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (6 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (4 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (5 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (7 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (8 ms) 8: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 8: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (9 ms) 8: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (86 ms total) 8: 8: [----------] Global test environment tear-down 8: [==========] 257 tests from 10 test cases ran. (476 ms total) 8: [ PASSED ] 257 tests. 8/27 Test #8: EwaldUnitTests ................... Passed 0.80 sec test 9 Start 9: FFTUnitTests 9: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/fft-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/FFTUnitTests.xml" 9: Test timeout computed to be: 30 9: -------------------------------------------------------------------------- 9: [[29251,1],0]: A high-performance Open MPI point-to-point messaging module 9: was unable to find any relevant network interfaces: 9: 9: Module: OpenFabrics (openib) 9: Host: codethink13-arm64 9: 9: Another transport will be used instead, although this may result in 9: lower performance. 9: 9: NOTE: You can disable this warning by setting the MCA parameter 9: btl_base_warn_component_unused to 0. 9: -------------------------------------------------------------------------- 9: [==========] Running 14 tests from 4 test cases. 9: [----------] Global test environment set-up. 9: [----------] 2 tests from ManyFFTTest 9: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (7 ms) 9: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test 9: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (15 ms) 9: [----------] 2 tests from ManyFFTTest (23 ms total) 9: 9: [----------] 1 test from FFTTest 9: [ RUN ] FFTTest.Real2DLength18_15Test 9: [ OK ] FFTTest.Real2DLength18_15Test (4 ms) 9: [----------] 1 test from FFTTest (4 ms total) 9: 9: [----------] 1 test from FFFTest3D 9: [ RUN ] FFFTest3D.Real5_6_9 9: [ OK ] FFFTest3D.Real5_6_9 (3 ms) 9: [----------] 1 test from FFFTest3D (4 ms total) 9: 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (2 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (1 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (0 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (11 ms) 9: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4 9: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (9 ms) 9: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (28 ms total) 9: 9: [----------] Global test environment tear-down 9: [==========] 14 tests from 4 test cases ran. (59 ms total) 9: [ PASSED ] 14 tests. 9/27 Test #9: FFTUnitTests ..................... Passed 0.31 sec test 10 Start 10: GpuUtilsUnitTests 10: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/gpu_utils-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/GpuUtilsUnitTests.xml" 10: Test timeout computed to be: 30 10: -------------------------------------------------------------------------- 10: [[29311,1],0]: A high-performance Open MPI point-to-point messaging module 10: was unable to find any relevant network interfaces: 10: 10: Module: OpenFabrics (openib) 10: Host: codethink13-arm64 10: 10: Another transport will be used instead, although this may result in 10: lower performance. 10: 10: NOTE: You can disable this warning by setting the MCA parameter 10: btl_base_warn_component_unused to 0. 10: -------------------------------------------------------------------------- 10: [==========] Running 60 tests from 19 test cases. 10: [----------] Global test environment set-up. 10: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int 10: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double 10: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/2 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks 10: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory 10: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms) 10: [----------] 2 tests from HostAllocatorTest/3 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/0 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/1 (0 ms total) 10: 10: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks 10: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork 10: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms) 10: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve 10: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms) 10: [----------] 3 tests from HostAllocatorTestCopyable/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMem/0.CreateVector 10: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Swap 10: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/0.Comparison 10: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/0 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMem/1.CreateVector 10: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Swap 10: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/1.Comparison 10: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/1 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMem/2.CreateVector 10: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Swap 10: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/2.Comparison 10: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/2 (0 ms total) 10: 10: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly 10: [ RUN ] HostAllocatorTestNoMem/3.CreateVector 10: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment 10: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction 10: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Swap 10: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms) 10: [ RUN ] HostAllocatorTestNoMem/3.Comparison 10: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms) 10: [----------] 5 tests from HostAllocatorTestNoMem/3 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (0 ms total) 10: 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms) 10: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction 10: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms) 10: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total) 10: 10: [----------] 1 test from HostAllocatorUntypedTest 10: [ RUN ] HostAllocatorUntypedTest.Comparison 10: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms) 10: [----------] 1 test from HostAllocatorUntypedTest (1 ms total) 10: 10: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/0.Move 10: [ OK ] AllocatorTest/0.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/0 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/1.Move 10: [ OK ] AllocatorTest/1.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/1 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator, gmx::HostAllocationPolicy> 10: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/2.Move 10: [ OK ] AllocatorTest/2.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/2 (0 ms total) 10: 10: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 10: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 10: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms) 10: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 10: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 10: [ RUN ] AllocatorTest/3.Move 10: [ OK ] AllocatorTest/3.Move (0 ms) 10: [----------] 4 tests from AllocatorTest/3 (1 ms total) 10: 10: [----------] Global test environment tear-down 10: [==========] 60 tests from 19 test cases ran. (2 ms total) 10: [ PASSED ] 60 tests. 10/27 Test #10: GpuUtilsUnitTests ................ Passed 0.29 sec test 11 Start 11: HardwareUnitTests 11: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/hardware-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/HardwareUnitTests.xml" 11: Test timeout computed to be: 30 11: -------------------------------------------------------------------------- 11: [[29589,1],0]: A high-performance Open MPI point-to-point messaging module 11: was unable to find any relevant network interfaces: 11: 11: Module: OpenFabrics (openib) 11: Host: codethink13-arm64 11: 11: Another transport will be used instead, although this may result in 11: lower performance. 11: 11: NOTE: You can disable this warning by setting the MCA parameter 11: btl_base_warn_component_unused to 0. 11: -------------------------------------------------------------------------- 11: [==========] Running 4 tests from 1 test case. 11: [----------] Global test environment set-up. 11: [----------] 4 tests from HardwareTopologyTest 11: [ RUN ] HardwareTopologyTest.Execute 11: [ OK ] HardwareTopologyTest.Execute (39 ms) 11: [ RUN ] HardwareTopologyTest.HwlocExecute 11: [ OK ] HardwareTopologyTest.HwlocExecute (36 ms) 11: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency 11: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (32 ms) 11: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency 11: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (28 ms) 11: [----------] 4 tests from HardwareTopologyTest (135 ms total) 11: 11: [----------] Global test environment tear-down 11: [==========] 4 tests from 1 test case ran. (135 ms total) 11: [ PASSED ] 4 tests. 11/27 Test #11: HardwareUnitTests ................ Passed 0.39 sec test 12 Start 12: MathUnitTests 12: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/math-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MathUnitTests.xml" 12: Test timeout computed to be: 30 12: -------------------------------------------------------------------------- 12: [[29618,1],0]: A high-performance Open MPI point-to-point messaging module 12: was unable to find any relevant network interfaces: 12: 12: Module: OpenFabrics (openib) 12: Host: codethink13-arm64 12: 12: Another transport will be used instead, although this may result in 12: lower performance. 12: 12: NOTE: You can disable this warning by setting the MCA parameter 12: btl_base_warn_component_unused to 0. 12: -------------------------------------------------------------------------- 12: [==========] Running 112 tests from 20 test cases. 12: [----------] Global test environment set-up. 12: [----------] 1 test from EmptyArrayRefWithPaddingTest 12: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest 12: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty 12: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms) 12: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/0 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total) 12: 12: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding 12: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks 12: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms) 12: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks 12: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms) 12: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total) 12: 12: [----------] 6 tests from StructureSimilarityTest 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho 12: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRho 12: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms) 12: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex 12: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms) 12: [----------] 6 tests from StructureSimilarityTest (0 ms total) 12: 12: [----------] 21 tests from FunctionTest 12: [ RUN ] FunctionTest.StaticLog2 12: [ OK ] FunctionTest.StaticLog2 (0 ms) 12: [ RUN ] FunctionTest.Log2I32Bit 12: [ OK ] FunctionTest.Log2I32Bit (0 ms) 12: [ RUN ] FunctionTest.Log2I64Bit 12: [ OK ] FunctionTest.Log2I64Bit (1 ms) 12: [ RUN ] FunctionTest.GreatestCommonDivisor 12: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms) 12: [ RUN ] FunctionTest.InvsqrtFloat 12: [ OK ] FunctionTest.InvsqrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvsqrtDouble 12: [ OK ] FunctionTest.InvsqrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvsqrtInteger 12: [ OK ] FunctionTest.InvsqrtInteger (0 ms) 12: [ RUN ] FunctionTest.InvcbrtFloat 12: [ OK ] FunctionTest.InvcbrtFloat (0 ms) 12: [ RUN ] FunctionTest.InvcbrtDouble 12: [ OK ] FunctionTest.InvcbrtDouble (0 ms) 12: [ RUN ] FunctionTest.InvcbrtInteger 12: [ OK ] FunctionTest.InvcbrtInteger (1 ms) 12: [ RUN ] FunctionTest.SixthrootFloat 12: [ OK ] FunctionTest.SixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.SixthrootDouble 12: [ OK ] FunctionTest.SixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.SixthrootInteger 12: [ OK ] FunctionTest.SixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootFloat 12: [ OK ] FunctionTest.InvsixthrootFloat (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootDouble 12: [ OK ] FunctionTest.InvsixthrootDouble (0 ms) 12: [ RUN ] FunctionTest.InvsixthrootInteger 12: [ OK ] FunctionTest.InvsixthrootInteger (0 ms) 12: [ RUN ] FunctionTest.Powers 12: [ OK ] FunctionTest.Powers (0 ms) 12: [ RUN ] FunctionTest.ErfInvFloat 12: [ OK ] FunctionTest.ErfInvFloat (1 ms) 12: [ RUN ] FunctionTest.ErfInvDouble 12: [ OK ] FunctionTest.ErfInvDouble (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (0 ms) 12: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble 12: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (0 ms) 12: [----------] 21 tests from FunctionTest (4 ms total) 12: 12: [----------] 2 tests from InvertMatrixTest 12: [ RUN ] InvertMatrixTest.IdentityIsImpotent 12: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertMatrixTest.ComputesInverse 12: [ OK ] InvertMatrixTest.ComputesInverse (0 ms) 12: [----------] 2 tests from InvertMatrixTest (0 ms total) 12: 12: [----------] 2 tests from InvertBoxMatrixTest 12: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent 12: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms) 12: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace 12: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms) 12: [----------] 2 tests from InvertBoxMatrixTest (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanCopyAssign 12: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanMoveAssign 12: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/0.CanSwap 12: [ OK ] PaddedVectorTest/0.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/0 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanCopyAssign 12: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanMoveAssign 12: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/1.CanSwap 12: [ OK ] PaddedVectorTest/1.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/1 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator 12: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanCopyAssign 12: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanMoveAssign 12: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/2.CanSwap 12: [ OK ] PaddedVectorTest/2.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/2 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanCopyAssign 12: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanMoveAssign 12: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/3.CanSwap 12: [ OK ] PaddedVectorTest/3.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/3 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator > 12: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanCopyAssign 12: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanMoveAssign 12: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/4.CanSwap 12: [ OK ] PaddedVectorTest/4.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/4 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanCopyAssign 12: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanMoveAssign 12: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/5.CanSwap 12: [ OK ] PaddedVectorTest/5.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/5 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanCopyAssign 12: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanMoveAssign 12: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/6.CanSwap 12: [ OK ] PaddedVectorTest/6.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/6 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator 12: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanCopyAssign 12: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanMoveAssign 12: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/7.CanSwap 12: [ OK ] PaddedVectorTest/7.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/7 (0 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (1 ms) 12: [ RUN ] PaddedVectorTest/8.CanCopyAssign 12: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanMoveAssign 12: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/8.CanSwap 12: [ OK ] PaddedVectorTest/8.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/8 (1 ms total) 12: 12: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 12: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves 12: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanCopyAssign 12: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanMoveAssign 12: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms) 12: [ RUN ] PaddedVectorTest/9.CanSwap 12: [ OK ] PaddedVectorTest/9.CanSwap (0 ms) 12: [----------] 4 tests from PaddedVectorTest/9 (0 ms total) 12: 12: [----------] 33 tests from RVecTest 12: [ RUN ] RVecTest.CanBeStoredInVector 12: [ OK ] RVecTest.CanBeStoredInVector (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms) 12: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec 12: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAsMutable_rvec 12: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Array 12: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms) 12: [ RUN ] RVecTest.CanAddRVecToRvec 12: [ OK ] RVecTest.CanAddRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanAddAssignRVecToRvec 12: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractRVecFromRvec 12: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec 12: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms) 12: [ RUN ] RVecTest.CanDotProductRVecByRvec 12: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanCrossProductRVecByRvec 12: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVecInplace 12: [ OK ] RVecTest.CanDivideRVecInplace (0 ms) 12: [ RUN ] RVecTest.CanScaleRVec 12: [ OK ] RVecTest.CanScaleRVec (0 ms) 12: [ RUN ] RVecTest.CanDivideRVec 12: [ OK ] RVecTest.CanDivideRVec (0 ms) 12: [ RUN ] RVecTest.CanDoUnitvFromRVec 12: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanSqLengthOfRVec 12: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanLengthOfRVec 12: [ OK ] RVecTest.CanLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToRVec 12: [ OK ] RVecTest.CanCastToRVec (0 ms) 12: [ RUN ] RVecTest.CanCastToDVec 12: [ OK ] RVecTest.CanCastToDVec (0 ms) 12: [ RUN ] RVecTest.CanLeftScalarMultiply 12: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanRightScalarMultiply 12: [ OK ] RVecTest.CanRightScalarMultiply (0 ms) 12: [ RUN ] RVecTest.CanGetUnitvFromRVec 12: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms) 12: [ RUN ] RVecTest.CanGetSqLengthOfRVec 12: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanGetLengthOfRVec 12: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoCrossProductOfRVec 12: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms) 12: [ RUN ] RVecTest.CanDoDotProductOfRVec 12: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms) 12: [ RUN ] RVecTest.WorksAs_dvec_Reference 12: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_ivec_Reference 12: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms) 12: [ RUN ] RVecTest.WorksAs_rvec_Reference 12: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms) 12: [ RUN ] RVecTest.CopyConstructorWorks 12: [ OK ] RVecTest.CopyConstructorWorks (0 ms) 12: [ RUN ] RVecTest.CopyAssignmentWorks 12: [ OK ] RVecTest.CopyAssignmentWorks (0 ms) 12: [ RUN ] RVecTest.MoveConstructorWorks 12: [ OK ] RVecTest.MoveConstructorWorks (0 ms) 12: [ RUN ] RVecTest.MoveAssignmentWorks 12: [ OK ] RVecTest.MoveAssignmentWorks (0 ms) 12: [----------] 33 tests from RVecTest (0 ms total) 12: 12: [----------] Global test environment tear-down 12: [==========] 112 tests from 20 test cases ran. (6 ms total) 12: [ PASSED ] 112 tests. 12/27 Test #12: MathUnitTests .................... Passed 0.27 sec test 13 Start 13: MdrunUtilityUnitTests 13: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/mdrunutility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdrunUtilityUnitTests.xml" 13: Test timeout computed to be: 30 13: -------------------------------------------------------------------------- 13: [[29648,1],0]: A high-performance Open MPI point-to-point messaging module 13: was unable to find any relevant network interfaces: 13: 13: Module: OpenFabrics (openib) 13: Host: codethink13-arm64 13: 13: Another transport will be used instead, although this may result in 13: lower performance. 13: 13: NOTE: You can disable this warning by setting the MCA parameter 13: btl_base_warn_component_unused to 0. 13: -------------------------------------------------------------------------- 13: [==========] Running 17 tests from 1 test case. 13: [----------] Global test environment set-up. 13: [----------] 17 tests from ThreadAffinityTest 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled 13: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported 13: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware 13: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (0 ms) 13: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride 13: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced 13: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread 13: NOTE: Affinity setting failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms) 13: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced 13: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (0 ms) 13: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads 13: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (6 ms) 13: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing 13: NOTE: Affinity setting for 1/2 threads failed. 13: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms) 13: [----------] 17 tests from ThreadAffinityTest (12 ms total) 13: 13: [----------] Global test environment tear-down 13: [==========] 17 tests from 1 test case ran. (12 ms total) 13: [ PASSED ] 17 tests. 13/27 Test #13: MdrunUtilityUnitTests ............ Passed 0.28 sec test 14 Start 14: MdrunUtilityMpiUnitTests 14: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi-dp/bin/mdrunutility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml" 14: Test timeout computed to be: 30 14: -------------------------------------------------------------------------- 14: [[29688,1],0]: A high-performance Open MPI point-to-point messaging module 14: was unable to find any relevant network interfaces: 14: 14: Module: OpenFabrics (openib) 14: Host: codethink13-arm64 14: 14: Another transport will be used instead, although this may result in 14: lower performance. 14: 14: NOTE: You can disable this warning by setting the MCA parameter 14: btl_base_warn_component_unused to 0. 14: -------------------------------------------------------------------------- 14: [==========] Running 13 tests from 2 test cases. 14: [----------] Global test environment set-up. 14: [----------] 6 tests from ThreadAffinityMultiRankTest 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode 14: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride 14: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes 14: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled 14: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (0 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (1 ms) 14: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce 14: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (0 ms) 14: [----------] 6 tests from ThreadAffinityMultiRankTest (3 ms total) 14: 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (1 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (0 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (81 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (57 ms) 14: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly 14: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (57 ms) 14: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (232 ms total) 14: 14: [----------] Global test environment tear-down 14: [==========] 13 tests from 2 test cases ran. (235 ms total) 14: [ PASSED ] 13 tests. 14: [codethink13-arm64:21873] 3 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics 14: [codethink13-arm64:21873] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 14/27 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.81 sec test 15 Start 15: OnlineHelpUnitTests 15: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/onlinehelp-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/OnlineHelpUnitTests.xml" 15: Test timeout computed to be: 30 15: -------------------------------------------------------------------------- 15: [[29505,1],0]: A high-performance Open MPI point-to-point messaging module 15: was unable to find any relevant network interfaces: 15: 15: Module: OpenFabrics (openib) 15: Host: codethink13-arm64 15: 15: Another transport will be used instead, although this may result in 15: lower performance. 15: 15: NOTE: You can disable this warning by setting the MCA parameter 15: btl_base_warn_component_unused to 0. 15: -------------------------------------------------------------------------- 15: [==========] Running 22 tests from 4 test cases. 15: [----------] Global test environment set-up. 15: [----------] 6 tests from TextTableFormatterTest 15: [ RUN ] TextTableFormatterTest.HandlesBasicCase 15: [ OK ] TextTableFormatterTest.HandlesBasicCase (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesIndentation 15: [ OK ] TextTableFormatterTest.HandlesIndentation (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines 15: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (1 ms) 15: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding 15: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms) 15: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns 15: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms) 15: [----------] 6 tests from TextTableFormatterTest (1 ms total) 15: 15: [----------] 3 tests from HelpManagerTest 15: [ RUN ] HelpManagerTest.HandlesRootTopic 15: [ OK ] HelpManagerTest.HandlesRootTopic (0 ms) 15: [ RUN ] HelpManagerTest.HandlesSubTopics 15: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms) 15: [ RUN ] HelpManagerTest.HandlesInvalidTopics 15: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms) 15: [----------] 3 tests from HelpManagerTest (0 ms total) 15: 15: [----------] 2 tests from HelpTopicFormattingTest 15: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic 15: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms) 15: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics 15: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (0 ms) 15: [----------] 2 tests from HelpTopicFormattingTest (1 ms total) 15: 15: [----------] 11 tests from HelpWriterContextTest 15: [ RUN ] HelpWriterContextTest.FormatsParagraphs 15: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs 15: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms) 15: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace 15: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralText 15: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms) 15: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation 15: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsBulletList 15: [ OK ] HelpWriterContextTest.FormatsBulletList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList 15: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsSimpleTable 15: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsGridTable 15: [ OK ] HelpWriterContextTest.FormatsGridTable (0 ms) 15: [ RUN ] HelpWriterContextTest.FormatsTitles 15: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms) 15: [----------] 11 tests from HelpWriterContextTest (1 ms total) 15: 15: [----------] Global test environment tear-down 15: [==========] 22 tests from 4 test cases ran. (3 ms total) 15: [ PASSED ] 22 tests. 15/27 Test #15: OnlineHelpUnitTests .............. Passed 0.26 sec test 16 Start 16: OptionsUnitTests 16: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/options-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/OptionsUnitTests.xml" 16: Test timeout computed to be: 30 16: -------------------------------------------------------------------------- 16: [[29551,1],0]: A high-performance Open MPI point-to-point messaging module 16: was unable to find any relevant network interfaces: 16: 16: Module: OpenFabrics (openib) 16: Host: codethink13-arm64 16: 16: Another transport will be used instead, although this may result in 16: lower performance. 16: 16: NOTE: You can disable this warning by setting the MCA parameter 16: btl_base_warn_component_unused to 0. 16: -------------------------------------------------------------------------- 16: [==========] Running 110 tests from 18 test cases. 16: [----------] Global test environment set-up. 16: [----------] 5 tests from AbstractOptionStorageTest 16: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish 16: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval 16: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition 16: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (0 ms) 16: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues 16: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (0 ms) 16: [----------] 5 tests from AbstractOptionStorageTest (1 ms total) 16: 16: [----------] 8 tests from FileNameOptionTest 16: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue 16: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption 16: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension 16: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (0 ms) 16: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix 16: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms) 16: [----------] 8 tests from FileNameOptionTest (0 ms total) 16: 16: [----------] 15 tests from FileNameOptionManagerTest 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension 16: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile 16: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (1 ms) 16: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified 16: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile 16: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms) 16: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking 16: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms) 16: [----------] 15 tests from FileNameOptionManagerTest (1 ms total) 16: 16: [----------] 1 test from OptionsTest 16: [ RUN ] OptionsTest.FailsOnNonsafeStorage 16: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms) 16: [----------] 1 test from OptionsTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerTest 16: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter 16: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue 16: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter 16: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMissingValue 16: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesExtraValue 16: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesGroups 16: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesSections 16: [ OK ] OptionsAssignerTest.HandlesSections (0 ms) 16: [ RUN ] OptionsAssignerTest.HandlesMultipleSources 16: [ OK ] OptionsAssignerTest.HandlesMultipleSources (1 ms) 16: [----------] 9 tests from OptionsAssignerTest (1 ms total) 16: 16: [----------] 4 tests from OptionsAssignerBooleanTest 16: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue 16: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue 16: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo 16: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms) 16: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue 16: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms) 16: [----------] 4 tests from OptionsAssignerBooleanTest (0 ms total) 16: 16: [----------] 13 tests from OptionsAssignerIntegerTest 16: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue 16: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow 16: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet 16: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet 16: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues 16: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.StoresToVector 16: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment 16: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms) 16: [----------] 13 tests from OptionsAssignerIntegerTest (0 ms total) 16: 16: [----------] 5 tests from OptionsAssignerDoubleTest 16: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue 16: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat 16: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms) 16: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue 16: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms) 16: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total) 16: 16: [----------] 9 tests from OptionsAssignerStringTest 16: [ RUN ] OptionsAssignerStringTest.StoresSingleValue 16: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray 16: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue 16: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue 16: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 9 tests from OptionsAssignerStringTest (0 ms total) 16: 16: [----------] 6 tests from OptionsAssignerEnumTest 16: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue 16: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues 16: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange 16: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms) 16: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector 16: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms) 16: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total) 16: 16: [----------] 8 tests from RepeatingOptionSectionTest 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption 16: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance 16: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue 16: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances 16: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault 16: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms) 16: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections 16: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms) 16: [----------] 8 tests from RepeatingOptionSectionTest (0 ms total) 16: 16: [----------] 1 test from TimeUnitManagerTest 16: [ RUN ] TimeUnitManagerTest.BasicOperations 16: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms) 16: [----------] 1 test from TimeUnitManagerTest (0 ms total) 16: 16: [----------] 4 tests from TimeUnitBehaviorTest 16: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue 16: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues 16: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources 16: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms) 16: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks 16: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (1 ms) 16: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total) 16: 16: [----------] 2 tests from TreeValueSupportAssignTest 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms) 16: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays 16: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms) 16: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total) 16: 16: [----------] 1 test from TreeValueSupportAssignErrorTest 16: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue 16: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms) 16: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total) 16: 16: [----------] 5 tests from TreeValueSupportCheckTest 16: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty 16: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree 16: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2 16: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms) 16: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue 16: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms) 16: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total) 16: 16: [----------] 6 tests from TreeValueSupportAdjustTest 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues 16: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues 16: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues 16: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms) 16: [ RUN ] TreeValueSupportAdjustTest.OrdersValues 16: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms) 16: [----------] 6 tests from TreeValueSupportAdjustTest (1 ms total) 16: 16: [----------] 8 tests from TreeValueSupportTest 16: [ RUN ] TreeValueSupportTest.SupportsBooleanOption 16: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsIntegerOption 16: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsInt64Option 16: [ OK ] TreeValueSupportTest.SupportsInt64Option (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsStringOption 16: [ OK ] TreeValueSupportTest.SupportsStringOption (1 ms) 16: [ RUN ] TreeValueSupportTest.SupportsFloatOption 16: [ OK ] TreeValueSupportTest.SupportsFloatOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsDoubleOption 16: [ OK ] TreeValueSupportTest.SupportsDoubleOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption 16: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms) 16: [ RUN ] TreeValueSupportTest.SupportsEnumOption 16: [ OK ] TreeValueSupportTest.SupportsEnumOption (0 ms) 16: [----------] 8 tests from TreeValueSupportTest (2 ms total) 16: 16: [----------] Global test environment tear-down 16: [==========] 110 tests from 18 test cases ran. (9 ms total) 16: [ PASSED ] 110 tests. 16/27 Test #16: OptionsUnitTests ................. Passed 0.33 sec test 17 Start 17: RandomUnitTests 17: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/random-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/RandomUnitTests.xml" 17: Test timeout computed to be: 30 17: -------------------------------------------------------------------------- 17: [[28806,1],0]: A high-performance Open MPI point-to-point messaging module 17: was unable to find any relevant network interfaces: 17: 17: Module: OpenFabrics (openib) 17: Host: codethink13-arm64 17: 17: Another transport will be used instead, although this may result in 17: lower performance. 17: 17: NOTE: You can disable this warning by setting the MCA parameter 17: btl_base_warn_component_unused to 0. 17: -------------------------------------------------------------------------- 17: [==========] Running 44 tests from 10 test cases. 17: [----------] Global test environment set-up. 17: [----------] 4 tests from ExponentialDistributionTest 17: [ RUN ] ExponentialDistributionTest.Output 17: [ OK ] ExponentialDistributionTest.Output (0 ms) 17: [ RUN ] ExponentialDistributionTest.Logical 17: [ OK ] ExponentialDistributionTest.Logical (0 ms) 17: [ RUN ] ExponentialDistributionTest.Reset 17: [ OK ] ExponentialDistributionTest.Reset (0 ms) 17: [ RUN ] ExponentialDistributionTest.AltParam 17: [ OK ] ExponentialDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from ExponentialDistributionTest (0 ms total) 17: 17: [----------] 4 tests from GammaDistributionTest 17: [ RUN ] GammaDistributionTest.Output 17: [ OK ] GammaDistributionTest.Output (0 ms) 17: [ RUN ] GammaDistributionTest.Logical 17: [ OK ] GammaDistributionTest.Logical (0 ms) 17: [ RUN ] GammaDistributionTest.Reset 17: [ OK ] GammaDistributionTest.Reset (0 ms) 17: [ RUN ] GammaDistributionTest.AltParam 17: [ OK ] GammaDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from GammaDistributionTest (0 ms total) 17: 17: [----------] 4 tests from NormalDistributionTest 17: [ RUN ] NormalDistributionTest.Output 17: [ OK ] NormalDistributionTest.Output (0 ms) 17: [ RUN ] NormalDistributionTest.Logical 17: [ OK ] NormalDistributionTest.Logical (1 ms) 17: [ RUN ] NormalDistributionTest.Reset 17: [ OK ] NormalDistributionTest.Reset (0 ms) 17: [ RUN ] NormalDistributionTest.AltParam 17: [ OK ] NormalDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from NormalDistributionTest (1 ms total) 17: 17: [----------] 1 test from SeedTest 17: [ RUN ] SeedTest.makeRandomSeed 17: [ OK ] SeedTest.makeRandomSeed (0 ms) 17: [----------] 1 test from SeedTest (0 ms total) 17: 17: [----------] 6 tests from TabulatedNormalDistributionTest 17: [ RUN ] TabulatedNormalDistributionTest.Output14 17: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Output16 17: [ OK ] TabulatedNormalDistributionTest.Output16 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14 17: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Logical 17: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.Reset 17: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms) 17: [ RUN ] TabulatedNormalDistributionTest.AltParam 17: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms) 17: [----------] 6 tests from TabulatedNormalDistributionTest (0 ms total) 17: 17: [----------] 1 test from TabulatedNormalDistributionTableTest 17: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties 17: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (3 ms) 17: [----------] 1 test from TabulatedNormalDistributionTableTest (3 ms total) 17: 17: [----------] 6 tests from ThreeFry2x64Test 17: [ RUN ] ThreeFry2x64Test.Logical 17: [ OK ] ThreeFry2x64Test.Logical (0 ms) 17: [ RUN ] ThreeFry2x64Test.InternalCounterSequence 17: [ OK ] ThreeFry2x64Test.InternalCounterSequence (0 ms) 17: [ RUN ] ThreeFry2x64Test.Reseed 17: [ OK ] ThreeFry2x64Test.Reseed (0 ms) 17: [ RUN ] ThreeFry2x64Test.Discard 17: [ OK ] ThreeFry2x64Test.Discard (0 ms) 17: [ RUN ] ThreeFry2x64Test.InvalidCounter 17: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms) 17: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter 17: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms) 17: [----------] 6 tests from ThreeFry2x64Test (0 ms total) 17: 17: [----------] 4 tests from UniformIntDistributionTest 17: [ RUN ] UniformIntDistributionTest.Output 17: [ OK ] UniformIntDistributionTest.Output (0 ms) 17: [ RUN ] UniformIntDistributionTest.Logical 17: [ OK ] UniformIntDistributionTest.Logical (0 ms) 17: [ RUN ] UniformIntDistributionTest.Reset 17: [ OK ] UniformIntDistributionTest.Reset (0 ms) 17: [ RUN ] UniformIntDistributionTest.AltParam 17: [ OK ] UniformIntDistributionTest.AltParam (0 ms) 17: [----------] 4 tests from UniformIntDistributionTest (1 ms total) 17: 17: [----------] 5 tests from UniformRealDistributionTest 17: [ RUN ] UniformRealDistributionTest.GenerateCanonical 17: [ OK ] UniformRealDistributionTest.GenerateCanonical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Output 17: [ OK ] UniformRealDistributionTest.Output (0 ms) 17: [ RUN ] UniformRealDistributionTest.Logical 17: [ OK ] UniformRealDistributionTest.Logical (0 ms) 17: [ RUN ] UniformRealDistributionTest.Reset 17: [ OK ] UniformRealDistributionTest.Reset (0 ms) 17: [ RUN ] UniformRealDistributionTest.AltParam 17: [ OK ] UniformRealDistributionTest.AltParam (0 ms) 17: [----------] 5 tests from UniformRealDistributionTest (0 ms total) 17: 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms) 17: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 17: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms) 17: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (1 ms total) 17: 17: [----------] Global test environment tear-down 17: [==========] 44 tests from 10 test cases ran. (6 ms total) 17: [ PASSED ] 44 tests. 17/27 Test #17: RandomUnitTests .................. Passed 0.30 sec test 18 Start 18: RestraintTests 18: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/restraintpotential-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/RestraintTests.xml" 18: Test timeout computed to be: 30 18: -------------------------------------------------------------------------- 18: [[28859,1],0]: A high-performance Open MPI point-to-point messaging module 18: was unable to find any relevant network interfaces: 18: 18: Module: OpenFabrics (openib) 18: Host: codethink13-arm64 18: 18: Another transport will be used instead, although this may result in 18: lower performance. 18: 18: NOTE: You can disable this warning by setting the MCA parameter 18: btl_base_warn_component_unused to 0. 18: -------------------------------------------------------------------------- 18: [==========] Running 1 test from 1 test case. 18: [----------] Global test environment set-up. 18: [----------] 1 test from RestraintManager 18: [ RUN ] RestraintManager.restraintList 18: [ OK ] RestraintManager.restraintList (0 ms) 18: [----------] 1 test from RestraintManager (0 ms total) 18: 18: [----------] Global test environment tear-down 18: [==========] 1 test from 1 test case ran. (0 ms total) 18: [ PASSED ] 1 test. 18/27 Test #18: RestraintTests ................... Passed 0.28 sec test 19 Start 19: TableUnitTests 19: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/table-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TableUnitTests.xml" 19: Test timeout computed to be: 30 19: -------------------------------------------------------------------------- 19: [[28895,1],0]: A high-performance Open MPI point-to-point messaging module 19: was unable to find any relevant network interfaces: 19: 19: Module: OpenFabrics (openib) 19: Host: codethink13-arm64 19: 19: Another transport will be used instead, although this may result in 19: lower performance. 19: 19: NOTE: You can disable this warning by setting the MCA parameter 19: btl_base_warn_component_unused to 0. 19: -------------------------------------------------------------------------- 19: [==========] Running 20 tests from 2 test cases. 19: [----------] Global test environment set-up. 19: [----------] 10 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable 19: [ RUN ] SplineTableTest/0.HandlesIncorrectInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectInput (3 ms) 19: [ RUN ] SplineTableTest/0.Sinc 19: [ OK ] SplineTableTest/0.Sinc (1 ms) 19: [ RUN ] SplineTableTest/0.LJ12 19: [ OK ] SplineTableTest/0.LJ12 (40 ms) 19: [ RUN ] SplineTableTest/0.PmeCorrection 19: [ OK ] SplineTableTest/0.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (5 ms) 19: [ RUN ] SplineTableTest/0.TwoFunctions 19: [ OK ] SplineTableTest/0.TwoFunctions (67 ms) 19: [ RUN ] SplineTableTest/0.ThreeFunctions 19: [ OK ] SplineTableTest/0.ThreeFunctions (73 ms) 19: [ RUN ] SplineTableTest/0.Simd 19: [ OK ] SplineTableTest/0.Simd (16 ms) 19: [ RUN ] SplineTableTest/0.SimdTwoFunctions 19: [ OK ] SplineTableTest/0.SimdTwoFunctions (66 ms) 19: [----------] 10 tests from SplineTableTest/0 (275 ms total) 19: 19: [----------] 10 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable 19: [ RUN ] SplineTableTest/1.HandlesIncorrectInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectInput (4 ms) 19: [ RUN ] SplineTableTest/1.Sinc 19: [ OK ] SplineTableTest/1.Sinc (2 ms) 19: [ RUN ] SplineTableTest/1.LJ12 19: [ OK ] SplineTableTest/1.LJ12 (86 ms) 19: [ RUN ] SplineTableTest/1.PmeCorrection 19: [ OK ] SplineTableTest/1.PmeCorrection (2 ms) 19: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput 19: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms) 19: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr 19: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (2 ms) 19: [ RUN ] SplineTableTest/1.TwoFunctions 19: [ OK ] SplineTableTest/1.TwoFunctions (172 ms) 19: [ RUN ] SplineTableTest/1.ThreeFunctions 19: [ OK ] SplineTableTest/1.ThreeFunctions (179 ms) 19: [ RUN ] SplineTableTest/1.Simd 19: [ OK ] SplineTableTest/1.Simd (41 ms) 19: [ RUN ] SplineTableTest/1.SimdTwoFunctions 19: [ OK ] SplineTableTest/1.SimdTwoFunctions (163 ms) 19: [----------] 10 tests from SplineTableTest/1 (653 ms total) 19: 19: [----------] Global test environment tear-down 19: [==========] 20 tests from 2 test cases ran. (928 ms total) 19: [ PASSED ] 20 tests. 19/27 Test #19: TableUnitTests ................... Passed 1.20 sec test 20 Start 20: TaskAssignmentUnitTests 20: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/taskassignment-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/TaskAssignmentUnitTests.xml" 20: Test timeout computed to be: 30 20: -------------------------------------------------------------------------- 20: [[28704,1],0]: A high-performance Open MPI point-to-point messaging module 20: was unable to find any relevant network interfaces: 20: 20: Module: OpenFabrics (openib) 20: Host: codethink13-arm64 20: 20: Another transport will be used instead, although this may result in 20: lower performance. 20: 20: NOTE: You can disable this warning by setting the MCA parameter 20: btl_base_warn_component_unused to 0. 20: -------------------------------------------------------------------------- 20: [==========] Running 3 tests from 1 test case. 20: [----------] Global test environment set-up. 20: [----------] 3 tests from GpuIdStringHandlingTest 20: [ RUN ] GpuIdStringHandlingTest.ParsingAndReconstructionWork 20: [ OK ] GpuIdStringHandlingTest.ParsingAndReconstructionWork (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.EmptyStringCanBeValid 20: [ OK ] GpuIdStringHandlingTest.EmptyStringCanBeValid (0 ms) 20: [ RUN ] GpuIdStringHandlingTest.InvalidInputsThrow 20: [ OK ] GpuIdStringHandlingTest.InvalidInputsThrow (0 ms) 20: [----------] 3 tests from GpuIdStringHandlingTest (0 ms total) 20: 20: [----------] Global test environment tear-down 20: [==========] 3 tests from 1 test case ran. (1 ms total) 20: [ PASSED ] 3 tests. 20/27 Test #20: TaskAssignmentUnitTests .......... Passed 0.25 sec test 21 Start 21: UtilityUnitTests 21: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/utility-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/UtilityUnitTests.xml" 21: Test timeout computed to be: 30 21: -------------------------------------------------------------------------- 21: [[28750,1],0]: A high-performance Open MPI point-to-point messaging module 21: was unable to find any relevant network interfaces: 21: 21: Module: OpenFabrics (openib) 21: Host: codethink13-arm64 21: 21: Another transport will be used instead, although this may result in 21: lower performance. 21: 21: NOTE: You can disable this warning by setting the MCA parameter 21: btl_base_warn_component_unused to 0. 21: -------------------------------------------------------------------------- 21: [==========] Running 325 tests from 52 test cases. 21: [----------] Global test environment set-up. 21: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/0.Move 21: [ OK ] AllocatorTest/0.Move (0 ms) 21: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/0 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/1.Move 21: [ OK ] AllocatorTest/1.Move (0 ms) 21: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/1 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/2.Move 21: [ OK ] AllocatorTest/2.Move (0 ms) 21: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/2 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator 21: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/3.Move 21: [ OK ] AllocatorTest/3.Move (0 ms) 21: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/3 (0 ms total) 21: 21: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator, gmx::AlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms) 21: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/4.Move 21: [ OK ] AllocatorTest/4.Move (0 ms) 21: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/4 (1 ms total) 21: 21: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator, gmx::PageAlignedAllocationPolicy> 21: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment 21: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment 21: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms) 21: [ RUN ] AllocatorTest/5.Move 21: [ OK ] AllocatorTest/5.Move (0 ms) 21: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory 21: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms) 21: [----------] 5 tests from AllocatorTest/5 (0 ms total) 21: 21: [----------] 1 test from AllocatorUntypedTest 21: [ RUN ] AllocatorUntypedTest.Comparison 21: [ OK ] AllocatorUntypedTest.Comparison (0 ms) 21: [----------] 1 test from AllocatorUntypedTest (0 ms total) 21: 21: [----------] 1 test from EmptyArrayRefTest 21: [ RUN ] EmptyArrayRefTest.IsEmpty 21: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyArrayRefTest (0 ms total) 21: 21: [----------] 1 test from EmptyConstArrayRefTest 21: [ RUN ] EmptyConstArrayRefTest.IsEmpty 21: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms) 21: [----------] 1 test from EmptyConstArrayRefTest (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/0 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (1 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/1 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/2 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/3 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/4 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/5 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/6 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/7 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/8 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/9 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/10 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/11 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/12 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/13 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/14 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/15 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/16 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/17 (1 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/18 (0 ms total) 21: 21: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef 21: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks 21: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms) 21: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks 21: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms) 21: [----------] 9 tests from ArrayRefTest/19 (0 ms total) 21: 21: [----------] 4 tests from KeyValueTreeSerializerTest 21: [ RUN ] KeyValueTreeSerializerTest.EmptyTree 21: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.SimpleObject 21: [ OK ] KeyValueTreeSerializerTest.SimpleObject (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (0 ms) 21: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects 21: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms) 21: [----------] 4 tests from KeyValueTreeSerializerTest (1 ms total) 21: 21: [----------] 6 tests from TreeValueTransformTest 21: [ RUN ] TreeValueTransformTest.SimpleTransforms 21: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive 21: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (0 ms) 21: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject 21: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromString 21: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms) 21: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings 21: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms) 21: [ RUN ] TreeValueTransformTest.ScopedTransformRules 21: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms) 21: [----------] 6 tests from TreeValueTransformTest (1 ms total) 21: 21: [----------] 1 test from TreeValueTransformErrorTest 21: [ RUN ] TreeValueTransformErrorTest.ConversionError 21: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms) 21: [----------] 1 test from TreeValueTransformErrorTest (0 ms total) 21: 21: [----------] 2 tests from RegexBasicTest 21: [ RUN ] RegexBasicTest.BasicMatchesWorkWhenSupported 21: [ OK ] RegexBasicTest.BasicMatchesWorkWhenSupported (0 ms) 21: [ RUN ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported 21: [ OK ] RegexBasicTest.MatchesForCharacterClassesWorkWhenSupported (0 ms) 21: [----------] 2 tests from RegexBasicTest (1 ms total) 21: 21: [----------] 5 tests from LoggerTest 21: [ RUN ] LoggerTest.EmptyLoggerWorks 21: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToStream 21: [ OK ] LoggerTest.LogsToStream (0 ms) 21: [ RUN ] LoggerTest.LogsToFile 21: [ OK ] LoggerTest.LogsToFile (1 ms) 21: [ RUN ] LoggerTest.LevelFilteringWorks 21: [ OK ] LoggerTest.LevelFilteringWorks (0 ms) 21: [ RUN ] LoggerTest.LogsToMultipleStreams 21: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms) 21: [----------] 5 tests from LoggerTest (1 ms total) 21: 21: [----------] 4 tests from MutexBasicTest 21: [ RUN ] MutexBasicTest.CanBeMade 21: [ OK ] MutexBasicTest.CanBeMade (0 ms) 21: [ RUN ] MutexBasicTest.CanBeLocked 21: [ OK ] MutexBasicTest.CanBeLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeTryLocked 21: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms) 21: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard 21: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms) 21: [----------] 4 tests from MutexBasicTest (0 ms total) 21: 21: [----------] 3 tests from MutexTaskTest 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (6 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (4 ms) 21: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread 21: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms) 21: [----------] 3 tests from MutexTaskTest (10 ms total) 21: 21: [----------] 4 tests from PathTest 21: [ RUN ] PathTest.StripSourcePrefixWorks 21: [ OK ] PathTest.StripSourcePrefixWorks (0 ms) 21: [ RUN ] PathTest.ConcatenateBeforeExtensionWorks 21: [ OK ] PathTest.ConcatenateBeforeExtensionWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathWorks 21: [ OK ] PathTest.GetParentPathWorks (0 ms) 21: [ RUN ] PathTest.GetParentPathAndBasenameWorks 21: [ OK ] PathTest.GetParentPathAndBasenameWorks (0 ms) 21: [----------] 4 tests from PathTest (0 ms total) 21: 21: [----------] 2 tests from PhysicalNodeCommunicatorTest 21: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 21: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (1 ms) 21: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 21: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms) 21: [----------] 2 tests from PhysicalNodeCommunicatorTest (1 ms total) 21: 21: [----------] 7 tests from StringUtilityTest 21: [ RUN ] StringUtilityTest.StartsWith 21: [ OK ] StringUtilityTest.StartsWith (0 ms) 21: [ RUN ] StringUtilityTest.EndsWith 21: [ OK ] StringUtilityTest.EndsWith (0 ms) 21: [ RUN ] StringUtilityTest.StripSuffixIfPresent 21: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms) 21: [ RUN ] StringUtilityTest.StripString 21: [ OK ] StringUtilityTest.StripString (0 ms) 21: [ RUN ] StringUtilityTest.SplitString 21: [ OK ] StringUtilityTest.SplitString (0 ms) 21: [ RUN ] StringUtilityTest.SplitDelimitedString 21: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms) 21: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString 21: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (0 ms) 21: [----------] 7 tests from StringUtilityTest (0 ms total) 21: 21: [----------] 2 tests from FormatStringTest 21: [ RUN ] FormatStringTest.HandlesBasicFormatting 21: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms) 21: [ RUN ] FormatStringTest.HandlesLongStrings 21: [ OK ] FormatStringTest.HandlesLongStrings (0 ms) 21: [----------] 2 tests from FormatStringTest (0 ms total) 21: 21: [----------] 1 test from StringFormatterTest 21: [ RUN ] StringFormatterTest.HandlesBasicFormatting 21: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms) 21: [----------] 1 test from StringFormatterTest (0 ms total) 21: 21: [----------] 1 test from formatAndJoinTest 21: [ RUN ] formatAndJoinTest.Works 21: [ OK ] formatAndJoinTest.Works (0 ms) 21: [----------] 1 test from formatAndJoinTest (0 ms total) 21: 21: [----------] 1 test from JoinStringsTest 21: [ RUN ] JoinStringsTest.Works 21: [ OK ] JoinStringsTest.Works (0 ms) 21: [----------] 1 test from JoinStringsTest (0 ms total) 21: 21: [----------] 6 tests from ReplaceAllTest 21: [ RUN ] ReplaceAllTest.HandlesEmptyStrings 21: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesNoMatches 21: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds 21: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (1 ms) 21: [ RUN ] ReplaceAllTest.HandlesMultipleMatches 21: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesWordBoundaries 21: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms) 21: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches 21: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms) 21: [----------] 6 tests from ReplaceAllTest (1 ms total) 21: 21: [----------] 10 tests from TextLineWrapperTest 21: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings 21: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace 21: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines 21: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectly 21: [ OK ] TextLineWrapperTest.WrapsCorrectly (0 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndent 21: [ OK ] TextLineWrapperTest.HandlesIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines 21: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesHangingIndent 21: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms) 21: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter 21: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms) 21: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace 21: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms) 21: [----------] 10 tests from TextLineWrapperTest (1 ms total) 21: 21: [----------] 6 tests from TextWriterTest 21: [ RUN ] TextWriterTest.WritesLines 21: [ OK ] TextWriterTest.WritesLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInParts 21: [ OK ] TextWriterTest.WritesLinesInParts (0 ms) 21: [ RUN ] TextWriterTest.WritesWrappedLines 21: [ OK ] TextWriterTest.WritesWrappedLines (0 ms) 21: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper 21: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms) 21: [ RUN ] TextWriterTest.TracksNewlines 21: [ OK ] TextWriterTest.TracksNewlines (0 ms) 21: [ RUN ] TextWriterTest.PreservesTrailingWhitespace 21: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms) 21: [----------] 6 tests from TextWriterTest (0 ms total) 21: 21: [----------] 1 test from TypeTraitsTest 21: [ RUN ] TypeTraitsTest.IsIntegralConstant 21: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms) 21: [----------] 1 test from TypeTraitsTest (0 ms total) 21: 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms) 21: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0 21: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms) 21: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total) 21: 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 21: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total) 21: 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms) 21: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 21: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms) 21: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total) 21: 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (1 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms) 21: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 21: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms) 21: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (1 ms total) 21: 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms) 21: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 21: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms) 21: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (0 ms total) 21: 21: [----------] Global test environment tear-down 21: [==========] 325 tests from 52 test cases ran. (24 ms total) 21: [ PASSED ] 325 tests. 21/27 Test #21: UtilityUnitTests ................. Passed 0.33 sec test 22 Start 22: UtilityMpiUnitTests 22: Test command: /usr/bin/mpiexec.openmpi "-np" "4" "/build/gromacs-2019.1/build/openmpi-dp/bin/utility-mpi-test" "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/UtilityMpiUnitTests.xml" 22: Test timeout computed to be: 30 22: -------------------------------------------------------------------------- 22: [[28772,1],0]: A high-performance Open MPI point-to-point messaging module 22: was unable to find any relevant network interfaces: 22: 22: Module: OpenFabrics (openib) 22: Host: codethink13-arm64 22: 22: Another transport will be used instead, although this may result in 22: lower performance. 22: 22: NOTE: You can disable this warning by setting the MCA parameter 22: btl_base_warn_component_unused to 0. 22: -------------------------------------------------------------------------- 22: [==========] Running 2 tests from 1 test case. 22: [----------] Global test environment set-up. 22: [----------] 2 tests from PhysicalNodeCommunicatorTest 22: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct 22: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (61 ms) 22: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier 22: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (48 ms) 22: [----------] 2 tests from PhysicalNodeCommunicatorTest (133 ms total) 22: 22: [----------] Global test environment tear-down 22: [==========] 2 tests from 1 test case ran. (133 ms total) 22: [ PASSED ] 2 tests. 22: [codethink13-arm64:22253] 3 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics 22: [codethink13-arm64:22253] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages 22/27 Test #22: UtilityMpiUnitTests .............. Passed 0.65 sec test 23 Start 23: FileIOTests 23: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/fileio-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/FileIOTests.xml" 23: Test timeout computed to be: 30 23: -------------------------------------------------------------------------- 23: [[29106,1],0]: A high-performance Open MPI point-to-point messaging module 23: was unable to find any relevant network interfaces: 23: 23: Module: OpenFabrics (openib) 23: Host: codethink13-arm64 23: 23: Another transport will be used instead, although this may result in 23: lower performance. 23: 23: NOTE: You can disable this warning by setting the MCA parameter 23: btl_base_warn_component_unused to 0. 23: -------------------------------------------------------------------------- 23: [==========] Running 17 tests from 4 test cases. 23: [----------] Global test environment set-up. 23: [----------] 2 tests from FileMD5Test 23: [ RUN ] FileMD5Test.CanComputeMD5 23: [ OK ] FileMD5Test.CanComputeMD5 (1 ms) 23: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong 23: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (0 ms) 23: [----------] 2 tests from FileMD5Test (1 ms total) 23: 23: [----------] 9 tests from ReadTest 23: [ RUN ] ReadTest.get_eint_ReadsInteger 23: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_eint64_ReadsInteger 23: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side '0.8' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms) 23: [ RUN ] ReadTest.get_eint64_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not an 23: integer value 23: 23: 23: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsInteger 23: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms) 23: [ RUN ] ReadTest.get_ereal_ReadsFloat 23: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms) 23: [ RUN ] ReadTest.get_ereal_WarnsAboutString 23: 23: ERROR 1 [file unknown, line 0]: 23: Right hand side 'hello' for parameter 'test' in parameter file is not a 23: real value 23: 23: 23: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms) 23: [----------] 9 tests from ReadTest (0 ms total) 23: 23: [----------] 2 tests from TngTest 23: [ RUN ] TngTest.CanOpenTngFile 23: [ OK ] TngTest.CanOpenTngFile (0 ms) 23: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal 23: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms) 23: [----------] 2 tests from TngTest (0 ms total) 23: 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (1 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (4 ms) 23: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 23: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (0 ms) 23: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (6 ms total) 23: 23: [----------] Global test environment tear-down 23: [==========] 17 tests from 4 test cases ran. (8 ms total) 23: [ PASSED ] 17 tests. 23/27 Test #23: FileIOTests ...................... Passed 0.30 sec test 24 Start 24: PullTest 24: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/pull-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/PullTest.xml" 24: Test timeout computed to be: 30 24: -------------------------------------------------------------------------- 24: [[29150,1],0]: A high-performance Open MPI point-to-point messaging module 24: was unable to find any relevant network interfaces: 24: 24: Module: OpenFabrics (openib) 24: Host: codethink13-arm64 24: 24: Another transport will be used instead, although this may result in 24: lower performance. 24: 24: NOTE: You can disable this warning by setting the MCA parameter 24: btl_base_warn_component_unused to 0. 24: -------------------------------------------------------------------------- 24: [==========] Running 5 tests from 1 test case. 24: [----------] Global test environment set-up. 24: [----------] 5 tests from PullTest 24: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox 24: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox 24: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzTricBox 24: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXyzLongBox 24: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms) 24: [ RUN ] PullTest.MaxPullDistanceXySkewedBox 24: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms) 24: [----------] 5 tests from PullTest (0 ms total) 24: 24: [----------] Global test environment tear-down 24: [==========] 5 tests from 1 test case ran. (0 ms total) 24: [ PASSED ] 5 tests. 24/27 Test #24: PullTest ......................... Passed 0.24 sec test 25 Start 25: AwhTest 25: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/awh-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/AwhTest.xml" 25: Test timeout computed to be: 30 25: -------------------------------------------------------------------------- 25: [[29169,1],0]: A high-performance Open MPI point-to-point messaging module 25: was unable to find any relevant network interfaces: 25: 25: Module: OpenFabrics (openib) 25: Host: codethink13-arm64 25: 25: Another transport will be used instead, although this may result in 25: lower performance. 25: 25: NOTE: You can disable this warning by setting the MCA parameter 25: btl_base_warn_component_unused to 0. 25: -------------------------------------------------------------------------- 25: [==========] Running 12 tests from 4 test cases. 25: [----------] Global test environment set-up. 25: [----------] 1 test from BiasTest 25: [ RUN ] BiasTest.DetectsCovering 25: [ OK ] BiasTest.DetectsCovering (1 ms) 25: [----------] 1 test from BiasTest (1 ms total) 25: 25: [----------] 1 test from gridTest 25: [ RUN ] gridTest.neighborhood 25: [ OK ] gridTest.neighborhood (2 ms) 25: [----------] 1 test from gridTest (2 ms total) 25: 25: [----------] 8 tests from WithParameters/BiasTest 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (1 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (0 ms) 25: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7 25: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (1 ms) 25: [----------] 8 tests from WithParameters/BiasTest (5 ms total) 25: 25: [----------] 2 tests from WithParameters/BiasStateTest 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (0 ms) 25: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1 25: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms) 25: [----------] 2 tests from WithParameters/BiasStateTest (1 ms total) 25: 25: [----------] Global test environment tear-down 25: [==========] 12 tests from 4 test cases ran. (9 ms total) 25: [ PASSED ] 12 tests. 25/27 Test #25: AwhTest .......................... Passed 0.27 sec test 26 Start 26: SimdUnitTests 26: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/simd-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/SimdUnitTests.xml" 26: Test timeout computed to be: 30 26: -------------------------------------------------------------------------- 26: [[28951,1],0]: A high-performance Open MPI point-to-point messaging module 26: was unable to find any relevant network interfaces: 26: 26: Module: OpenFabrics (openib) 26: Host: codethink13-arm64 26: 26: Another transport will be used instead, although this may result in 26: lower performance. 26: 26: NOTE: You can disable this warning by setting the MCA parameter 26: btl_base_warn_component_unused to 0. 26: -------------------------------------------------------------------------- 26: [==========] Running 236 tests from 19 test cases. 26: [----------] Global test environment set-up. 26: [----------] 6 tests from SimdBootstrapTest 26: [ RUN ] SimdBootstrapTest.loadStore 26: [ OK ] SimdBootstrapTest.loadStore (0 ms) 26: [ RUN ] SimdBootstrapTest.loadU 26: [ OK ] SimdBootstrapTest.loadU (0 ms) 26: [ RUN ] SimdBootstrapTest.storeU 26: [ OK ] SimdBootstrapTest.storeU (0 ms) 26: [ RUN ] SimdBootstrapTest.loadStoreI 26: [ OK ] SimdBootstrapTest.loadStoreI (0 ms) 26: [ RUN ] SimdBootstrapTest.loadUI 26: [ OK ] SimdBootstrapTest.loadUI (0 ms) 26: [ RUN ] SimdBootstrapTest.storeUI 26: [ OK ] SimdBootstrapTest.storeUI (0 ms) 26: [----------] 6 tests from SimdBootstrapTest (0 ms total) 26: 26: [----------] 1 test from SimdTest 26: [ RUN ] SimdTest.GmxAligned 26: [ OK ] SimdTest.GmxAligned (0 ms) 26: [----------] 1 test from SimdTest (0 ms total) 26: 26: [----------] 42 tests from SimdFloatingpointTest 26: [ RUN ] SimdFloatingpointTest.setZero 26: [ OK ] SimdFloatingpointTest.setZero (0 ms) 26: [ RUN ] SimdFloatingpointTest.set 26: [ OK ] SimdFloatingpointTest.set (0 ms) 26: [ RUN ] SimdFloatingpointTest.add 26: [ OK ] SimdFloatingpointTest.add (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskAdd 26: [ OK ] SimdFloatingpointTest.maskAdd (0 ms) 26: [ RUN ] SimdFloatingpointTest.sub 26: [ OK ] SimdFloatingpointTest.sub (0 ms) 26: [ RUN ] SimdFloatingpointTest.mul 26: [ OK ] SimdFloatingpointTest.mul (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzMul 26: [ OK ] SimdFloatingpointTest.maskzMul (0 ms) 26: [ RUN ] SimdFloatingpointTest.fma 26: [ OK ] SimdFloatingpointTest.fma (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzFma 26: [ OK ] SimdFloatingpointTest.maskzFma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fms 26: [ OK ] SimdFloatingpointTest.fms (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnma 26: [ OK ] SimdFloatingpointTest.fnma (0 ms) 26: [ RUN ] SimdFloatingpointTest.fnms 26: [ OK ] SimdFloatingpointTest.fnms (0 ms) 26: [ RUN ] SimdFloatingpointTest.abs 26: [ OK ] SimdFloatingpointTest.abs (0 ms) 26: [ RUN ] SimdFloatingpointTest.neg 26: [ OK ] SimdFloatingpointTest.neg (0 ms) 26: [ RUN ] SimdFloatingpointTest.and 26: [ OK ] SimdFloatingpointTest.and (0 ms) 26: [ RUN ] SimdFloatingpointTest.or 26: [ OK ] SimdFloatingpointTest.or (0 ms) 26: [ RUN ] SimdFloatingpointTest.xor 26: [ OK ] SimdFloatingpointTest.xor (0 ms) 26: [ RUN ] SimdFloatingpointTest.andNot 26: [ OK ] SimdFloatingpointTest.andNot (0 ms) 26: [ RUN ] SimdFloatingpointTest.max 26: [ OK ] SimdFloatingpointTest.max (0 ms) 26: [ RUN ] SimdFloatingpointTest.min 26: [ OK ] SimdFloatingpointTest.min (0 ms) 26: [ RUN ] SimdFloatingpointTest.round 26: [ OK ] SimdFloatingpointTest.round (0 ms) 26: [ RUN ] SimdFloatingpointTest.roundMode 26: [ OK ] SimdFloatingpointTest.roundMode (0 ms) 26: [ RUN ] SimdFloatingpointTest.trunc 26: [ OK ] SimdFloatingpointTest.trunc (0 ms) 26: [ RUN ] SimdFloatingpointTest.frexp 26: [ OK ] SimdFloatingpointTest.frexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.ldexp 26: [ OK ] SimdFloatingpointTest.ldexp (0 ms) 26: [ RUN ] SimdFloatingpointTest.rsqrt 26: [ OK ] SimdFloatingpointTest.rsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRsqrt 26: [ OK ] SimdFloatingpointTest.maskzRsqrt (0 ms) 26: [ RUN ] SimdFloatingpointTest.rcp 26: [ OK ] SimdFloatingpointTest.rcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.maskzRcp 26: [ OK ] SimdFloatingpointTest.maskzRcp (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpEqAndSelectByMask 26: [ OK ] SimdFloatingpointTest.cmpEqAndSelectByMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.selectByNotMask 26: [ OK ] SimdFloatingpointTest.selectByNotMask (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpNe 26: [ OK ] SimdFloatingpointTest.cmpNe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLe 26: [ OK ] SimdFloatingpointTest.cmpLe (0 ms) 26: [ RUN ] SimdFloatingpointTest.cmpLt 26: [ OK ] SimdFloatingpointTest.cmpLt (0 ms) 26: [ RUN ] SimdFloatingpointTest.testBits 26: [ OK ] SimdFloatingpointTest.testBits (0 ms) 26: [ RUN ] SimdFloatingpointTest.andB 26: [ OK ] SimdFloatingpointTest.andB (0 ms) 26: [ RUN ] SimdFloatingpointTest.orB 26: [ OK ] SimdFloatingpointTest.orB (0 ms) 26: [ RUN ] SimdFloatingpointTest.anyTrueB 26: [ OK ] SimdFloatingpointTest.anyTrueB (0 ms) 26: [ RUN ] SimdFloatingpointTest.blend 26: [ OK ] SimdFloatingpointTest.blend (0 ms) 26: [ RUN ] SimdFloatingpointTest.reduce 26: [ OK ] SimdFloatingpointTest.reduce (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtFloat2Double 26: [ OK ] SimdFloatingpointTest.cvtFloat2Double (0 ms) 26: [ RUN ] SimdFloatingpointTest.cvtDouble2Float 26: [ OK ] SimdFloatingpointTest.cvtDouble2Float (0 ms) 26: [----------] 42 tests from SimdFloatingpointTest (0 ms total) 26: 26: [----------] 13 tests from SimdFloatingpointUtilTest 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUTranspose3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterStoreU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterStoreU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterIncrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping 26: [ OK ] SimdFloatingpointUtilTest.transposeScatterDecrU3Overlapping (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.expandScalarsToTriplets 26: [ OK ] SimdFloatingpointUtilTest.expandScalarsToTriplets (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose4 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 26: [ OK ] SimdFloatingpointUtilTest.gatherLoadUBySimdIntTranspose2 (0 ms) 26: [ RUN ] SimdFloatingpointUtilTest.reduceIncr4Sum 26: [ OK ] SimdFloatingpointUtilTest.reduceIncr4Sum (0 ms) 26: [----------] 13 tests from SimdFloatingpointUtilTest (0 ms total) 26: 26: [----------] 3 tests from SimdVectorOperationsTest 26: [ RUN ] SimdVectorOperationsTest.iprod 26: [ OK ] SimdVectorOperationsTest.iprod (0 ms) 26: [ RUN ] SimdVectorOperationsTest.norm2 26: [ OK ] SimdVectorOperationsTest.norm2 (0 ms) 26: [ RUN ] SimdVectorOperationsTest.cprod 26: [ OK ] SimdVectorOperationsTest.cprod (0 ms) 26: [----------] 3 tests from SimdVectorOperationsTest (0 ms total) 26: 26: [----------] 45 tests from SimdMathTest 26: [ RUN ] SimdMathTest.copysign 26: [ OK ] SimdMathTest.copysign (0 ms) 26: [ RUN ] SimdMathTest.invsqrt 26: [ OK ] SimdMathTest.invsqrt (1 ms) 26: [ RUN ] SimdMathTest.maskzInvsqrt 26: [ OK ] SimdMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdMathTest.invsqrtPair 26: [ OK ] SimdMathTest.invsqrtPair (2 ms) 26: [ RUN ] SimdMathTest.sqrt 26: [ OK ] SimdMathTest.sqrt (2 ms) 26: [ RUN ] SimdMathTest.sqrtUnsafe 26: [ OK ] SimdMathTest.sqrtUnsafe (1 ms) 26: [ RUN ] SimdMathTest.inv 26: [ OK ] SimdMathTest.inv (1 ms) 26: [ RUN ] SimdMathTest.maskzInv 26: [ OK ] SimdMathTest.maskzInv (0 ms) 26: [ RUN ] SimdMathTest.log 26: [ OK ] SimdMathTest.log (2 ms) 26: [ RUN ] SimdMathTest.exp2 26: [ OK ] SimdMathTest.exp2 (3 ms) 26: [ RUN ] SimdMathTest.exp2Unsafe 26: [ OK ] SimdMathTest.exp2Unsafe (5 ms) 26: [ RUN ] SimdMathTest.exp 26: [ OK ] SimdMathTest.exp (3 ms) 26: [ RUN ] SimdMathTest.expUnsafe 26: [ OK ] SimdMathTest.expUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erf 26: [ OK ] SimdMathTest.erf (2 ms) 26: [ RUN ] SimdMathTest.erfc 26: [ OK ] SimdMathTest.erfc (2 ms) 26: [ RUN ] SimdMathTest.sin 26: [ OK ] SimdMathTest.sin (2 ms) 26: [ RUN ] SimdMathTest.cos 26: [ OK ] SimdMathTest.cos (3 ms) 26: [ RUN ] SimdMathTest.tan 26: [ OK ] SimdMathTest.tan (7 ms) 26: [ RUN ] SimdMathTest.asin 26: [ OK ] SimdMathTest.asin (6 ms) 26: [ RUN ] SimdMathTest.acos 26: [ OK ] SimdMathTest.acos (1 ms) 26: [ RUN ] SimdMathTest.atan 26: [ OK ] SimdMathTest.atan (1 ms) 26: [ RUN ] SimdMathTest.atan2 26: [ OK ] SimdMathTest.atan2 (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrection 26: [ OK ] SimdMathTest.pmeForceCorrection (3 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrection 26: [ OK ] SimdMathTest.pmePotentialCorrection (2 ms) 26: [ RUN ] SimdMathTest.invsqrtSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdMathTest.invsqrtPairSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracy 26: [ OK ] SimdMathTest.sqrtSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.sqrtSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.sqrtSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.invSingleAccuracy 26: [ OK ] SimdMathTest.invSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.logSingleAccuracy 26: [ OK ] SimdMathTest.logSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracy 26: [ OK ] SimdMathTest.exp2SingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.exp2SingleAccuracyUnsafe 26: [ OK ] SimdMathTest.exp2SingleAccuracyUnsafe (2 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracy 26: [ OK ] SimdMathTest.expSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.expSingleAccuracyUnsafe 26: [ OK ] SimdMathTest.expSingleAccuracyUnsafe (1 ms) 26: [ RUN ] SimdMathTest.erfSingleAccuracy 26: [ OK ] SimdMathTest.erfSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.erfcSingleAccuracy 26: [ OK ] SimdMathTest.erfcSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.sinSingleAccuracy 26: [ OK ] SimdMathTest.sinSingleAccuracy (3 ms) 26: [ RUN ] SimdMathTest.cosSingleAccuracy 26: [ OK ] SimdMathTest.cosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.tanSingleAccuracy 26: [ OK ] SimdMathTest.tanSingleAccuracy (7 ms) 26: [ RUN ] SimdMathTest.asinSingleAccuracy 26: [ OK ] SimdMathTest.asinSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.acosSingleAccuracy 26: [ OK ] SimdMathTest.acosSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.atanSingleAccuracy 26: [ OK ] SimdMathTest.atanSingleAccuracy (1 ms) 26: [ RUN ] SimdMathTest.atan2SingleAccuracy 26: [ OK ] SimdMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmeForceCorrectionSingleAccuracy (2 ms) 26: [ RUN ] SimdMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdMathTest.pmePotentialCorrectionSingleAccuracy (2 ms) 26: [----------] 45 tests from SimdMathTest (90 ms total) 26: 26: [----------] 1 test from EmptyArrayRefTest 26: [ RUN ] EmptyArrayRefTest.IsEmpty 26: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms) 26: [----------] 1 test from EmptyArrayRefTest (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/0.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/0.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/0 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/1.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/1.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/1 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/2.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/2.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/2 (0 ms total) 26: 26: [----------] 3 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks 26: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayRefWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayRefWorks (0 ms) 26: [ RUN ] ArrayRefTest/3.ConstructFromArrayWorks 26: [ OK ] ArrayRefTest/3.ConstructFromArrayWorks (0 ms) 26: [----------] 3 tests from ArrayRefTest/3 (0 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/0.Assignment 26: [ OK ] ArrayRefReadWriteTest/0.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/0 (1 ms total) 26: 26: [----------] 1 test from ArrayRefReadWriteTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefReadWriteTest/1.Assignment 26: [ OK ] ArrayRefReadWriteTest/1.Assignment (0 ms) 26: [----------] 1 test from ArrayRefReadWriteTest/1 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/0, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/0.Basic 26: [ OK ] ArrayRefArithmeticTest/0.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/0 (0 ms total) 26: 26: [----------] 1 test from ArrayRefArithmeticTest/1, where TypeParam = gmx::ArrayRef 26: [ RUN ] ArrayRefArithmeticTest/1.Basic 26: [ OK ] ArrayRefArithmeticTest/1.Basic (0 ms) 26: [----------] 1 test from ArrayRefArithmeticTest/1 (0 ms total) 26: 26: [----------] 23 tests from SimdIntegerTest 26: [ RUN ] SimdIntegerTest.setZero 26: [ OK ] SimdIntegerTest.setZero (0 ms) 26: [ RUN ] SimdIntegerTest.set 26: [ OK ] SimdIntegerTest.set (0 ms) 26: [ RUN ] SimdIntegerTest.add 26: [ OK ] SimdIntegerTest.add (0 ms) 26: [ RUN ] SimdIntegerTest.sub 26: [ OK ] SimdIntegerTest.sub (0 ms) 26: [ RUN ] SimdIntegerTest.mul 26: [ OK ] SimdIntegerTest.mul (0 ms) 26: [ RUN ] SimdIntegerTest.and 26: [ OK ] SimdIntegerTest.and (0 ms) 26: [ RUN ] SimdIntegerTest.andNot 26: [ OK ] SimdIntegerTest.andNot (0 ms) 26: [ RUN ] SimdIntegerTest.or 26: [ OK ] SimdIntegerTest.or (0 ms) 26: [ RUN ] SimdIntegerTest.xor 26: [ OK ] SimdIntegerTest.xor (0 ms) 26: [ RUN ] SimdIntegerTest.extract 26: [ OK ] SimdIntegerTest.extract (0 ms) 26: [ RUN ] SimdIntegerTest.cvtR2I 26: [ OK ] SimdIntegerTest.cvtR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvttR2I 26: [ OK ] SimdIntegerTest.cvttR2I (0 ms) 26: [ RUN ] SimdIntegerTest.cvtI2R 26: [ OK ] SimdIntegerTest.cvtI2R (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpEqAndSelectNotMask 26: [ OK ] SimdIntegerTest.cmpEqAndSelectNotMask (0 ms) 26: [ RUN ] SimdIntegerTest.cmpLt 26: [ OK ] SimdIntegerTest.cmpLt (0 ms) 26: [ RUN ] SimdIntegerTest.testBits 26: [ OK ] SimdIntegerTest.testBits (0 ms) 26: [ RUN ] SimdIntegerTest.andB 26: [ OK ] SimdIntegerTest.andB (0 ms) 26: [ RUN ] SimdIntegerTest.orB 26: [ OK ] SimdIntegerTest.orB (0 ms) 26: [ RUN ] SimdIntegerTest.anyTrue 26: [ OK ] SimdIntegerTest.anyTrue (0 ms) 26: [ RUN ] SimdIntegerTest.blend 26: [ OK ] SimdIntegerTest.blend (0 ms) 26: [ RUN ] SimdIntegerTest.cvtB2IB 26: [ OK ] SimdIntegerTest.cvtB2IB (0 ms) 26: [ RUN ] SimdIntegerTest.cvtIB2B 26: [ OK ] SimdIntegerTest.cvtIB2B (0 ms) 26: [----------] 23 tests from SimdIntegerTest (0 ms total) 26: 26: [----------] 41 tests from SimdScalarTest 26: [ RUN ] SimdScalarTest.load 26: [ OK ] SimdScalarTest.load (0 ms) 26: [ RUN ] SimdScalarTest.loadU 26: [ OK ] SimdScalarTest.loadU (0 ms) 26: [ RUN ] SimdScalarTest.store 26: [ OK ] SimdScalarTest.store (0 ms) 26: [ RUN ] SimdScalarTest.storeU 26: [ OK ] SimdScalarTest.storeU (0 ms) 26: [ RUN ] SimdScalarTest.setZero 26: [ OK ] SimdScalarTest.setZero (0 ms) 26: [ RUN ] SimdScalarTest.andNot 26: [ OK ] SimdScalarTest.andNot (0 ms) 26: [ RUN ] SimdScalarTest.fma 26: [ OK ] SimdScalarTest.fma (0 ms) 26: [ RUN ] SimdScalarTest.fms 26: [ OK ] SimdScalarTest.fms (0 ms) 26: [ RUN ] SimdScalarTest.fnma 26: [ OK ] SimdScalarTest.fnma (0 ms) 26: [ RUN ] SimdScalarTest.fnms 26: [ OK ] SimdScalarTest.fnms (0 ms) 26: [ RUN ] SimdScalarTest.maskAdd 26: [ OK ] SimdScalarTest.maskAdd (0 ms) 26: [ RUN ] SimdScalarTest.maskzMul 26: [ OK ] SimdScalarTest.maskzMul (0 ms) 26: [ RUN ] SimdScalarTest.maskzFma 26: [ OK ] SimdScalarTest.maskzFma (0 ms) 26: [ RUN ] SimdScalarTest.abs 26: [ OK ] SimdScalarTest.abs (0 ms) 26: [ RUN ] SimdScalarTest.max 26: [ OK ] SimdScalarTest.max (0 ms) 26: [ RUN ] SimdScalarTest.min 26: [ OK ] SimdScalarTest.min (0 ms) 26: [ RUN ] SimdScalarTest.round 26: [ OK ] SimdScalarTest.round (0 ms) 26: [ RUN ] SimdScalarTest.trunc 26: [ OK ] SimdScalarTest.trunc (0 ms) 26: [ RUN ] SimdScalarTest.reduce 26: [ OK ] SimdScalarTest.reduce (0 ms) 26: [ RUN ] SimdScalarTest.testBits 26: [ OK ] SimdScalarTest.testBits (0 ms) 26: [ RUN ] SimdScalarTest.anyTrue 26: [ OK ] SimdScalarTest.anyTrue (0 ms) 26: [ RUN ] SimdScalarTest.selectByMask 26: [ OK ] SimdScalarTest.selectByMask (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMask 26: [ OK ] SimdScalarTest.selectByNotMask (0 ms) 26: [ RUN ] SimdScalarTest.blend 26: [ OK ] SimdScalarTest.blend (0 ms) 26: [ RUN ] SimdScalarTest.cvtR2I 26: [ OK ] SimdScalarTest.cvtR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvttR2I 26: [ OK ] SimdScalarTest.cvttR2I (0 ms) 26: [ RUN ] SimdScalarTest.cvtI2R 26: [ OK ] SimdScalarTest.cvtI2R (0 ms) 26: [ RUN ] SimdScalarTest.cvtF2D 26: [ OK ] SimdScalarTest.cvtF2D (0 ms) 26: [ RUN ] SimdScalarTest.cvtD2D 26: [ OK ] SimdScalarTest.cvtD2D (0 ms) 26: [ RUN ] SimdScalarTest.loadI 26: [ OK ] SimdScalarTest.loadI (0 ms) 26: [ RUN ] SimdScalarTest.loadUI 26: [ OK ] SimdScalarTest.loadUI (0 ms) 26: [ RUN ] SimdScalarTest.storeI 26: [ OK ] SimdScalarTest.storeI (0 ms) 26: [ RUN ] SimdScalarTest.storeUI 26: [ OK ] SimdScalarTest.storeUI (0 ms) 26: [ RUN ] SimdScalarTest.andNotI 26: [ OK ] SimdScalarTest.andNotI (0 ms) 26: [ RUN ] SimdScalarTest.testBitsI 26: [ OK ] SimdScalarTest.testBitsI (0 ms) 26: [ RUN ] SimdScalarTest.selectByMaskI 26: [ OK ] SimdScalarTest.selectByMaskI (0 ms) 26: [ RUN ] SimdScalarTest.selectByNotMaskI 26: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms) 26: [ RUN ] SimdScalarTest.blendI 26: [ OK ] SimdScalarTest.blendI (0 ms) 26: [ RUN ] SimdScalarTest.cvtB2IB 26: [ OK ] SimdScalarTest.cvtB2IB (0 ms) 26: [ RUN ] SimdScalarTest.cvtIB2B 26: [ OK ] SimdScalarTest.cvtIB2B (0 ms) 26: [ RUN ] SimdScalarTest.expandScalarsToTriplets 26: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms) 26: [----------] 41 tests from SimdScalarTest (0 ms total) 26: 26: [----------] 8 tests from SimdScalarUtilTest 26: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU 26: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU 26: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU 26: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose 26: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms) 26: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum 26: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms) 26: [----------] 8 tests from SimdScalarUtilTest (1 ms total) 26: 26: [----------] 37 tests from SimdScalarMathTest 26: [ RUN ] SimdScalarMathTest.copysign 26: [ OK ] SimdScalarMathTest.copysign (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPair 26: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms) 26: [ RUN ] SimdScalarMathTest.inv 26: [ OK ] SimdScalarMathTest.inv (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrt 26: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms) 26: [ RUN ] SimdScalarMathTest.log 26: [ OK ] SimdScalarMathTest.log (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2 26: [ OK ] SimdScalarMathTest.exp2 (0 ms) 26: [ RUN ] SimdScalarMathTest.exp 26: [ OK ] SimdScalarMathTest.exp (0 ms) 26: [ RUN ] SimdScalarMathTest.erf 26: [ OK ] SimdScalarMathTest.erf (0 ms) 26: [ RUN ] SimdScalarMathTest.erfc 26: [ OK ] SimdScalarMathTest.erfc (0 ms) 26: [ RUN ] SimdScalarMathTest.sincos 26: [ OK ] SimdScalarMathTest.sincos (0 ms) 26: [ RUN ] SimdScalarMathTest.sin 26: [ OK ] SimdScalarMathTest.sin (0 ms) 26: [ RUN ] SimdScalarMathTest.cos 26: [ OK ] SimdScalarMathTest.cos (0 ms) 26: [ RUN ] SimdScalarMathTest.tan 26: [ OK ] SimdScalarMathTest.tan (0 ms) 26: [ RUN ] SimdScalarMathTest.asin 26: [ OK ] SimdScalarMathTest.asin (0 ms) 26: [ RUN ] SimdScalarMathTest.acos 26: [ OK ] SimdScalarMathTest.acos (0 ms) 26: [ RUN ] SimdScalarMathTest.atan 26: [ OK ] SimdScalarMathTest.atan (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2 26: [ OK ] SimdScalarMathTest.atan2 (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrection 26: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrection 26: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms) 26: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy 26: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.invSingleAccuracy 26: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy 26: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.logSingleAccuracy 26: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy 26: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.expSingleAccuracy 26: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy 26: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy 26: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.sinSingleAccuracy 26: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.cosSingleAccuracy 26: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.tanSingleAccuracy 26: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.asinSingleAccuracy 26: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.acosSingleAccuracy 26: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atanSingleAccuracy 26: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy 26: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms) 26: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy 26: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms) 26: [----------] 37 tests from SimdScalarMathTest (0 ms total) 26: 26: [----------] Global test environment tear-down 26: [==========] 236 tests from 19 test cases ran. (93 ms total) 26: [ PASSED ] 236 tests. 26/27 Test #26: SimdUnitTests .................... Passed 0.38 sec test 27 Start 27: CompatibilityHelpersTests 27: Test command: /build/gromacs-2019.1/build/openmpi-dp/bin/compat-test "--gtest_output=xml:/build/gromacs-2019.1/build/openmpi-dp/Testing/Temporary/CompatibilityHelpersTests.xml" 27: Test timeout computed to be: 30 27: -------------------------------------------------------------------------- 27: [[29005,1],0]: A high-performance Open MPI point-to-point messaging module 27: was unable to find any relevant network interfaces: 27: 27: Module: OpenFabrics (openib) 27: Host: codethink13-arm64 27: 27: Another transport will be used instead, although this may result in 27: lower performance. 27: 27: NOTE: You can disable this warning by setting the MCA parameter 27: btl_base_warn_component_unused to 0. 27: -------------------------------------------------------------------------- 27: [==========] Running 6 tests from 6 test cases. 27: [----------] Global test environment set-up. 27: [----------] 1 test from CompatibilityHelper 27: [ RUN ] CompatibilityHelper.MakeUniqueCompiles 27: [ OK ] CompatibilityHelper.MakeUniqueCompiles (0 ms) 27: [----------] 1 test from CompatibilityHelper (0 ms total) 27: 27: [----------] 1 test from NotNullConstruction 27: [ RUN ] NotNullConstruction.Works 27: [ OK ] NotNullConstruction.Works (0 ms) 27: [----------] 1 test from NotNullConstruction (1 ms total) 27: 27: [----------] 1 test from NotNullCasting 27: [ RUN ] NotNullCasting.Works 27: [ OK ] NotNullCasting.Works (0 ms) 27: [----------] 1 test from NotNullCasting (0 ms total) 27: 27: [----------] 1 test from NotNullAssignment 27: [ RUN ] NotNullAssignment.Works 27: [ OK ] NotNullAssignment.Works (0 ms) 27: [----------] 1 test from NotNullAssignment (0 ms total) 27: 27: [----------] 1 test from MakeNotNull 27: [ RUN ] MakeNotNull.Works 27: [ OK ] MakeNotNull.Works (0 ms) 27: [----------] 1 test from MakeNotNull (0 ms total) 27: 27: [----------] 1 test from NotNull 27: [ RUN ] NotNull.WorksInContainers 27: [ OK ] NotNull.WorksInContainers (0 ms) 27: [----------] 1 test from NotNull (0 ms total) 27: 27: [----------] Global test environment tear-down 27: [==========] 6 tests from 6 test cases ran. (1 ms total) 27: [ PASSED ] 6 tests. 27/27 Test #27: CompatibilityHelpersTests ........ Passed 0.27 sec 100% tests passed, 0 tests failed out of 27 Label Time Summary: GTest = 10.25 sec*proc (27 tests) MpiTest = 1.80 sec*proc (3 tests) UnitTest = 10.25 sec*proc (27 tests) Total Test time (real) = 10.66 sec touch build-openmpi dh_testdir # Build speedy, stripped-down version just for documentation generation. # Derived from admin/build-docs.sh (mkdir -p build/documentation ; cd build/documentation; \ cmake /build/gromacs-2019.1 -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) -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Performing Test CXXFLAG_STD_CXX0X -- Performing Test CXXFLAG_STD_CXX0X - Success -- Performing Test CXX11_SUPPORTED -- Performing Test CXX11_SUPPORTED - Success -- Performing Test CXX11_STDLIB_PRESENT -- Performing Test CXX11_STDLIB_PRESENT - Success -- Performing Test CFLAGS_PRAGMA -- Performing Test CFLAGS_PRAGMA - 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_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 regex.h -- Looking for include file regex.h - found -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for sysconf -- Looking for sysconf - found -- Looking for nice -- Looking for nice - found -- Looking for fsync -- Looking for fsync - found -- Looking for _fileno -- Looking for _fileno - not found -- Looking for fileno -- Looking for fileno - found -- Looking for _commit -- Looking for _commit - not found -- Looking for sigaction -- Looking for sigaction - found -- Performing Test HAVE_BUILTIN_CLZ -- Performing Test HAVE_BUILTIN_CLZ - Success -- Performing Test HAVE_BUILTIN_CLZLL -- Performing Test HAVE_BUILTIN_CLZLL - Success -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for feenableexcept in m -- Looking for feenableexcept in m - found -- Looking for fedisableexcept in m -- Looking for fedisableexcept in m - found -- Checking for sched.h GNU affinity API -- Performing Test sched_affinity_compile -- Performing Test sched_affinity_compile - Success -- Looking for include file mm_malloc.h -- Looking for include file mm_malloc.h - not found -- Looking for include file malloc.h -- Looking for include file malloc.h - found -- Looking for include file xmmintrin.h -- Looking for include file xmmintrin.h - not 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 -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- hwloc version: 1.11.12 -- Found Hwloc: /usr/lib/aarch64-linux-gnu/libhwloc.so (found suitable version "1.11.12", minimum required is "1.5") -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Atomic operations found -- Performing Test PTHREAD_SETAFFINITY -- Performing Test PTHREAD_SETAFFINITY - 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 - 0 -- Detected build CPU stepping - 1 -- Detected build CPU features - neon neon_asimd -- Disabling RDTSCP support -- 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 -- Looking for C++ include regex -- Looking for C++ include regex - found -- Checking for system XDR support -- Checking for system XDR support - present -- 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 -- pkg-config could not detect fftw3f, trying generic detection -- 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_ - found -- A library with LAPACK API found. -- Checking for dlopen -- Performing Test HAVE_DLOPEN -- Performing Test HAVE_DLOPEN - Success -- Checking for dlopen - found -- Using dynamic plugins (e.g VMD-supported file formats) -- Checking for suitable VMD version -- VMD plugins not found. Path to VMD can be set with VMDDIR. -- Using default binary suffix: "" -- Using default library suffix: "" CMake Warning at cmake/gmxTestImageMagick.cmake:69 (MESSAGE): Could not convert sample image, ImageMagick convert can not be used Call Stack (most recent call first): CMakeLists.txt:908 (GMX_TEST_IMAGEMAGICK) -- Found PythonInterp: /usr/bin/python2.7 (found suitable version "2.7.16", minimum required is "2.7") -- Found LATEX: /usr/bin/latex -- Performing Test HAS_NO_UNUSED_VARIABLE -- Performing Test HAS_NO_UNUSED_VARIABLE - Success -- Performing Test HAS_NO_UNUSED -- Performing Test HAS_NO_UNUSED - Success -- Performing Test HAS_NO_MISSING_DECL -- Performing Test HAS_NO_MISSING_DECL - Success -- Performing Test HAS_NO_MISSING_PROTO -- Performing Test HAS_NO_MISSING_PROTO - Failed -- Performing Test HAS_NO_MSVC_UNUSED -- Performing Test HAS_NO_MSVC_UNUSED - Failed -- Performing Test HAS_DECL_IN_SOURCE -- Performing Test HAS_DECL_IN_SOURCE - Failed -- Check if the system is big endian -- Searching 16 bit integer -- Using unsigned short -- Check if the system is big endian - little endian -- Looking for inttypes.h -- Looking for inttypes.h - found -- Configuring done -- Generating done -- Build files have been written to: /build/gromacs-2019.1/build/documentation /usr/bin/make -j8 gmx -C build/documentation make[1]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 gmx make[2]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 68 /usr/bin/make -f CMakeFiles/Makefile2 src/programs/CMakeFiles/gmx.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= Scanning dependencies of target view_objlib Scanning dependencies of target lmfit_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /build/gromacs-2019.1/src/programs/view/view.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /build/gromacs-2019.1/src/external/lmfit/lmmin.cpp Scanning dependencies of target tng_io_zlib Scanning dependencies of target mdrun_objlib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /build/gromacs-2019.1/src/programs/mdrun/mdrun.cpp make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/adler32.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/adler32.c Scanning dependencies of target tng_io_obj make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwlzh.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/bwt.c Scanning dependencies of target libgromacs_external make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/eigensolver.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/eigensolver.cpp Scanning dependencies of target libgromacs_generated cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/compress.c make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/crc32.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/crc32.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/coder.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/deflate.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/deflate.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/dict.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/fixpoint.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/gmx_arpack.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffman.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/huffmem.c make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 0%] Built target view_objlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/lz77.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/merge_sort.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/mtf.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/rle.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/tng_compress.c make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/vals16.c [ 0%] Built target lmfit_objlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 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CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc2.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/compression/xtc3.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inffast.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/inffast.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inflate.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/inflate.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/include -I/build/gromacs-2019.1/build/documentation/tng/include -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /build/gromacs-2019.1/src/external/tng_io/src/lib/md5.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/inftrees.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/inftrees.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/matrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/matrix.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 0%] Built target mdrun_objlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/trees.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/trees.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/nrjac.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/nrjac.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/uncompr.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/uncompr.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/tng_io/external/zlib -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/tng_io_zlib.dir/__/external/tng_io/external/zlib/zutil.c.o -c /build/gromacs-2019.1/src/external/tng_io/external/zlib/zutil.c cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/linearalgebra/sparsematrix.cpp.o -c /build/gromacs-2019.1/src/gromacs/linearalgebra/sparsematrix.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/lock.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/lock.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/pthreads.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem 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tng_io_zlib cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/p2p_protocol.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 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-DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/type.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/type.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/scan.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/scan.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/numa_malloc.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs_external.dir/__/external/thread_mpi/src/once.cpp.o -c /build/gromacs-2019.1/src/external/thread_mpi/src/once.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_c.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 2%] Built target libgromacs_external cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCSTab_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3P1_c.cpp /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c: In function 'tng_time_get_str': /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:15188:24: warning: '%02d' directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 16 [-Wformat-truncation=] "%4d-%02d-%02d %02d:%02d:%02d", ^~~~ In file included from /usr/include/stdio.h:873, from /build/gromacs-2019.1/src/external/tng_io/include/tng/tng_io.h:308, from /build/gromacs-2019.1/src/external/tng_io/src/lib/tng_io.c:20: /usr/include/aarch64-linux-gnu/bits/stdio2.h:67:10: note: '__builtin___snprintf_chk' output between 20 and 72 bytes into a destination of size 24 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecCoul_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomP1P1_c.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 5%] Built target tng_io_obj cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJEwSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 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/build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEw_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src 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-Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_c.cpp 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/usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwBham_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwCSTab_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW4W4_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomP1P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW3W3_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwNone_GeomW4P1_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src 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-Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp.o -c /build/gromacs-2019.1/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/scanner.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/scanner.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -o CMakeFiles/libgromacs_generated.dir/selection/parser.cpp.o -c /build/gromacs-2019.1/src/gromacs/selection/parser.cpp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 23%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI=10.5281/zenodo.2564764 -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= Scanning dependencies of target libgromacs make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem 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CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineoptionsmodule.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /build/gromacs-2019.1/src/gromacs/commandline/cmdlineparser.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 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&& /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src 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-fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o 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/build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_F_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_F_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_prune.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_search.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_search.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -fPIC -o CMakeFiles/libgromacs.dir/mdlib/nbnxn_tuning.cpp.o -c /build/gromacs-2019.1/src/gromacs/mdlib/nbnxn_tuning.cpp cd /build/gromacs-2019.1/build/documentation/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/build/gromacs-2019.1/build/documentation/src -I/build/gromacs-2019.1/src -I/build/gromacs-2019.1/src/external/lmfit -isystem /build/gromacs-2019.1/src/external/thread_mpi/include -isystem /build/gromacs-2019.1/src/external/tng_io/include -isystem /build/gromacs-2019.1/build/documentation/tng/include -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. 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-ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /build/gromacs-2019.1/src/programs/legacymodules.cpp cd /build/gromacs-2019.1/build/documentation/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/gromacs-2019.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wno-unknown-pragmas -g -fno-inline -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o -o ../../bin/gmx -Wl,-rpath,"\$ORIGIN/../lib" ../../lib/libgromacs.so.4.0.0 -lm make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target gmx make[3]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[1]: Leaving directory '/build/gromacs-2019.1/build/documentation' # Generate PDF /usr/bin/make -j8 manual -C build/documentation make[1]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 manual make[2]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 docs/manual/CMakeFiles/manual.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/manual /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/manual /build/gromacs-2019.1/build/documentation/docs/manual/CMakeFiles/manual.dir/DependInfo.cmake --color= Scanning dependencies of target manual make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/manual/CMakeFiles/manual.dir/build.make docs/manual/CMakeFiles/manual.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/manual && /usr/bin/cmake -E echo "Cannot build PDF manual, because a working form of ImageMagick convert is not available" Cannot build PDF manual, because a working form of ImageMagick convert is not available make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' Built target manual make[3]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[1]: Leaving directory '/build/gromacs-2019.1/build/documentation' # Generate HTML # This sometimes seems to work the *second* time? Still trying to trace it down. /usr/bin/make -j8 webpage -C build/documentation || \ (echo "===== Failed to build documentation, retrying." ; /usr/bin/make -j8 webpage -C build/documentation ) make[1]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/make -f CMakeFiles/Makefile2 webpage make[2]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/documentation --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 81 /usr/bin/make -f CMakeFiles/Makefile2 docs/CMakeFiles/webpage.dir/all make[3]: Entering directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/DependInfo.cmake --color= /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-version.dir/DependInfo.cmake --color= /usr/bin/make -f docs/CMakeFiles/sphinx-image-conversion.dir/build.make docs/CMakeFiles/sphinx-image-conversion.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-image-conversion.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_zlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend Scanning dependencies of target sphinx-image-conversion make[4]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-image-conversion-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_zlib.dir/build.make src/gromacs/CMakeFiles/tng_io_zlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_zlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build Scanning dependencies of target doxygen-version make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-version.dir/build.make docs/doxygen/CMakeFiles/doxygen-version.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/docs/doxygen/Doxyfile-version.cmakein -D VERSION_OUT=Doxyfile-version -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' Scanning dependencies of target doxygen-source-timestamp /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build [ 0%] Built target lmfit_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build.make docs/doxygen/CMakeFiles/doxygen-source-timestamp.dir/build [ 0%] Built target tng_io_zlib make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-source-timestamp.txt /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend [ 2%] Built target tng_io_obj /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/depend make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build [ 2%] Built target mdrun_objlib make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-input-rst.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' Scanning dependencies of target sphinx-input-rst [ 2%] Built target doxygen-source-timestamp make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-input-rst.dir/build.make docs/CMakeFiles/sphinx-input-rst.dir/build make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/xvgr.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/xvgr.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -D VERSION_VARIABLES=/build/gromacs-2019.1/build/documentation/VersionInfo.cmake -D VERSION_CMAKEIN=/build/gromacs-2019.1/docs/conf-vars.py.cmakein -D VERSION_OUT=/build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf-vars.py -D SPHINX_EXTENSION_PATH=/build/gromacs-2019.1/docs -D RELENG_PATH= -D IMAGE_CONVERT_STRING=impossible -D EXPECTED_DOXYGEN_VERSION=1.8.5 -D EXPECTED_SPHINX_VERSION=1.6.1 -D CMAKE_MINIMUM_REQUIRED_VERSION=3.4.3 -D REQUIRED_CUDA_VERSION=7.0 -D REQUIRED_OPENCL_MIN_VERSION=1.2 -D REQUIRED_CUDA_COMPUTE_CAPABILITY=3.0 -D REGRESSIONTEST_VERSION=2019.1 -D SOURCE_MD5SUM=unknown -D REGRESSIONTEST_MD5SUM_STRING=unknown -D GMX_TNG_MINIMUM_REQUIRED_VERSION=1.7.10 -D GMX_LMFIT_REQUIRED_VERSION=7.0 -D "GMX_MANUAL_DOI_STRING=Please reference this documentation as https://doi.org/10.5281/zenodo.2564761." -D "GMX_SOURCE_DOI_STRING=To cite the source code for this release, please cite https://doi.org/10.5281/zenodo.2564764." -P /build/gromacs-2019.1/cmake/gmxConfigureVersionInfo.cmake [ 17%] Built target libgromacs_generated cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/index.rst make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/download.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/download.rst [ 17%] Built target view_objlib cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/conf.py /build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf.py cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch Doxyfile-version cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/links.dat /build/gromacs-2019.1/build/documentation/docs/sphinx-input/links.dat cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-input/conf-vars.py cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/build-system.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/build-system.rst [ 19%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/change-management.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/change-management.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/commitstyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/commitstyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/documentation-generation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/documentation-generation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/contribute.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/contribute.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/doxygen.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/doxygen.rst [ 19%] Built target sphinx-image-conversion cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/error-handling.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/error-handling.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/formatting.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/formatting.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/gmxtree.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/gmxtree.rst make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/includestyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/includestyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/jenkins.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/jenkins.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/known-issues.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/known-issues.rst [ 19%] Built target doxygen-version cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/language-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/language-features.rst /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/depend cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/naming.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/naming.rst make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-xml.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/overview.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/overview.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/physical_validation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/physical_validation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/redmine-states.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/redmine-states.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/relocatable-binaries.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/relocatable-binaries.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/reportstyle.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/reportstyle.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/style.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/style.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/testutils.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/testutils.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/tools.rst Scanning dependencies of target doxygen-xml cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/uncrustify.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/uncrustify.rst make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-xml.dir/build.make docs/doxygen/CMakeFiles/doxygen-xml.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/fragments/doxygen-links.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/fragments/doxygen-links.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/beginners.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/beginners.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/topology.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/topology.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/special.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/special.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/how-to/visualize.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/visualize.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/install-guide/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/install-guide/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/2019.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/2019.1.rst cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=xml -P RunDoxygen.cmake cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/tools.rst NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/removed-functionality.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/removed-functionality.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/deprecated-functionality.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/deprecated-functionality.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/portability.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/portability.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2019/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2019/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.6.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.6.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.5.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.5.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.4.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.4.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.3.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.3.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.2.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.2.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/2018.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/2018.1.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/tools.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/removed-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/removed-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/portability.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/portability.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2018/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2018/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.5.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.5.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.4.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.4.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.3.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.3.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.2.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.2.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/2016.1.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/2016.1.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/highlights.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/highlights.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/new-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/new-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/tools.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/tools.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/bugs-fixed.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/bugs-fixed.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/removed-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/removed-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/2016/major/miscellaneous.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/2016/major/miscellaneous.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/release-notes/older/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/release-notes/older/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/cmdline.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/cmdline.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/cutoff-schemes.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/cutoff-schemes.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/deprecation-policy.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/deprecation-policy.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/environment-variables.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/environment-variables.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/faq.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/faq.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/floating-point.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/floating-point.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/flow.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/flow.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/force-fields.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/force-fields.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/getting-started.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/getting-started.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/index.rst make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/gromacs /build/gromacs-2019.1/build/documentation/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/managing-simulations.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/managing-simulations.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdp-options.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdrun-features.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdrun-features.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/mdrun-performance.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdrun-performance.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/run-time-errors.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/run-time-errors.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/security.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/security.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/system-preparation.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/system-preparation.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/user-guide/terminology.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/jenkins-howto.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/jenkins-howto.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/dev-manual/releng/jenkins-ui.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/dev-manual/releng/jenkins-ui.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/index.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/preface.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/preface.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/introduction.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/introduction.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/definitions.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/definitions.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/particle-type.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/parameter-files.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/parameter-files.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/molecule-definition.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/constraint-algorithm-section.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/constraint-algorithm-section.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/pdb2gmx-input-files.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/topology-file-formats.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/topologies/force-field-organization.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/force-field-organization.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/file-formats.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/file-formats.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/run-parameters.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/run-parameters.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/details.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/averages.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/averages.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/references.rst /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/references.rst cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/peregrine.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/peregrine.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/adress.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/adress.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E copy /build/gromacs-2019.1/docs/reference-manual/plots/plotje.png /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/plots/plotje.png cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-input-rst-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 29%] Built target sphinx-input-rst /usr/bin/make -f docs/CMakeFiles/sphinx-input.dir/build.make docs/CMakeFiles/sphinx-input.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-input.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-input make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f 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-E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/src/programs /build/gromacs-2019.1/build/documentation/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 93%] Built target gmx /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/sphinx-programs.dir/DependInfo.cmake --color= Scanning dependencies of target sphinx-programs make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/sphinx-programs.dir/build.make docs/CMakeFiles/sphinx-programs.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /usr/bin/cmake -E make_directory onlinehelp cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /build/gromacs-2019.1/build/documentation/bin/gmx -quiet help -export rst cd /build/gromacs-2019.1/build/documentation/docs/sphinx-input && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/sphinx-programs-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 95%] Built target sphinx-programs /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/webpage-sphinx.dir/DependInfo.cmake --color= Scanning dependencies of target webpage-sphinx make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage-sphinx.dir/build.make docs/CMakeFiles/webpage-sphinx.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/sphinx-input/_static cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/sphinx-build -q -E -b html -w sphinx-html.log -d /build/gromacs-2019.1/build/documentation/docs/_doctrees /build/gromacs-2019.1/build/documentation/docs/sphinx-input /build/gromacs-2019.1/build/documentation/docs/html The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:195: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:205: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(const EmptyArrayRef&)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:195: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(pointer, pointer)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:205: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(const EmptyArrayRef&)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copybrief or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/fileio/warninp.h:117: warning: @copydetails or @copydoc target 'warning_error_and_exit(warninp_t, const char *, int, const char *, int);' not found /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `g' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `m' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `x' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `e' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `s' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/restraint/restraintpotential.h:356: warning: Unexpected character `:' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-xml-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 96%] Built target doxygen-xml /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/dep-graphs-dot.dir/DependInfo.cmake --color= /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-user.dir/DependInfo.cmake --color= Scanning dependencies of target dep-graphs-dot make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build.make docs/doxygen/CMakeFiles/dep-graphs-dot.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/python2.7 /build/gromacs-2019.1/docs/doxygen/graphbuilder.py -S /build/gromacs-2019.1 -B /build/gromacs-2019.1/build/documentation --ignore-cycles /build/gromacs-2019.1/docs/doxygen/cycle-suppressions.txt -o /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs Scanning dependencies of target doxygen-user make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-user.dir/build.make docs/doxygen/CMakeFiles/doxygen-user.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=user -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... Scanning source tree... Reading source files... Reading Doxygen XML files... libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/algorithms' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/functions' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/special' /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/index.rst:25: WARNING: toctree contains reference to nonexisting document u'reference-manual/analysis' The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5145: warning: documented symbol `if *lworkl(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5352: warning: documented symbol `if *rvec(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-user-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 96%] Built target doxygen-user Writing graphs... cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/dep-graphs-dot-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 97%] Built target dep-graphs-dot /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/depend /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-lib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-full.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-lib make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-lib.dir/build.make docs/doxygen/CMakeFiles/doxygen-lib.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs Scanning dependencies of target doxygen-full make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-full.dir/build.make docs/doxygen/CMakeFiles/doxygen-full.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E make_directory /build/gromacs-2019.1/build/documentation/docs/doxygen/depgraphs cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=lib -P RunDoxygen.cmake cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -DDOCTYPE=full -P RunDoxygen.cmake NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... NOTE: You are using Doxygen version 1.8.13. The documentation is designed for 1.8.5. Other versions may or may not work, but very likely produce extra warnings. Running Doxygen... libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed /build/gromacs-2019.1/build/documentation/docs/sphinx-input/how-to/special.rst:84: WARNING: undefined label: ff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/definitions.rst:284: WARNING: undefined label: virial (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: lj (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:241: WARNING: undefined label: coul (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:255: WARNING: undefined label: lj (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/details.rst:257: WARNING: undefined label: coul (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/introduction.rst:306: WARNING: undefined label: em (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies.rst:4: WARNING: undefined label: ff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:79: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:100: WARNING: undefined label: dgimplement (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/molecule-definition.rst:134: WARNING: undefined label: groupconcept (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:63: WARNING: undefined label: virtualsites (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/particle-type.rst:68: WARNING: undefined label: virtualsites (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:56: WARNING: undefined label: defaultgroups (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/pdb2gmx-input-files.rst:151: WARNING: undefined label: charmmff (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:552: WARNING: undefined label: positionrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:556: WARNING: undefined label: dihedralrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:563: WARNING: equation not found: eqndphi /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:563: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:566: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:569: WARNING: equation not found: eqndihre /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:577: WARNING: undefined label: groupconcept (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:577: WARNING: undefined label: usinggroups (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:716: WARNING: undefined label: positionrestraint (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:724: WARNING: undefined label: fecalc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:724: WARNING: undefined label: feia (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/reference-manual/topologies/topology-file-formats.rst:865: WARNING: undefined label: pull (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/mdp-options.rst:3066: WARNING: undefined label: electric fields (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:72: WARNING: undefined label: pbc (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:135: WARNING: undefined label: temp-coupling (if the link has no caption the label must precede a section header) /build/gromacs-2019.1/build/documentation/docs/sphinx-input/user-guide/terminology.rst:370: WARNING: undefined label: md (if the link has no caption the label must precede a section header) make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 98%] Built target webpage-sphinx libpath/shortest.c:324: triangulation failed libpath/shortest.c:324: triangulation failed The following warnings were produced by Doxygen: /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5145: warning: documented symbol `if *lworkl(* ncv<< 3)' was not declared or defined. /build/gromacs-2019.1/src/gromacs/linearalgebra/gmx_arpack.cpp:5352: warning: documented symbol `if *rvec(* ncv<< 3)' was not declared or defined. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-lib-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [ 98%] Built target doxygen-lib The following warnings were produced by Doxygen: warning: Included by graph for 'gmxpre.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Include graph for 'runner.cpp' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'arrayref.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'basedefinitions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'classhelpers.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'exceptions.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'fatalerror.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'gmxassert.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'real.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'smalloc.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'stringutil.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'refdata.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. warning: Included by graph for 'testasserts.h' not generated, too many nodes. Consider increasing DOT_GRAPH_MAX_NODES. /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `g' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `m' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `x' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `e' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `s' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `t' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/selection/selection.h:351: warning: Unexpected character `:' /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/abstractoptionstorage.h:146: warning: @copydetails or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:268: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copybrief or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/utility/arrayref.h:276: warning: @copydetails or @copydoc target 'ArrayRef::fromArray()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< bool > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< double > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< float > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int64_t > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< int > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:104: warning: @copybrief or @copydoc target 'OptionInfo::defaultValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found :1: warning: @copybrief or @copydoc target 'OptionInfo::normalizeValues()' not found /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:331: warning: Member normalizeValues(const std::vector< Variant > &values) const override (function) of class OptionStorageTemplateSimple< std::string > is not documented. /build/gromacs-2019.1/src/gromacs/options/optionstoragetemplate.h:106: warning: @copybrief or @copydoc target 'OptionInfo::defaultValuesAsStrings()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copybrief or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/applied-forces/electricfield.cpp:175: warning: @copydetails or @copydoc target 'IForceProvider::calculateForces()' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copybrief or @copydoc target 'ArrayRef::ArrayRef(U)' not found /build/gromacs-2019.1/src/gromacs/simd/simd_memory.h:207: warning: @copydetails or @copydoc target 'ArrayRef::ArrayRef(U)' not found cd /build/gromacs-2019.1/build/documentation/docs/doxygen && /usr/bin/cmake -E touch /build/gromacs-2019.1/build/documentation/docs/doxygen/doxygen-full-timestamp.txt make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target doxygen-full /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs/doxygen /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs/doxygen /build/gromacs-2019.1/build/documentation/docs/doxygen/CMakeFiles/doxygen-all.dir/DependInfo.cmake --color= Scanning dependencies of target doxygen-all make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/doxygen/CMakeFiles/doxygen-all.dir/build.make docs/doxygen/CMakeFiles/doxygen-all.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' make[4]: Nothing to be done for 'docs/doxygen/CMakeFiles/doxygen-all.dir/build'. make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target doxygen-all /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/depend make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/docs /build/gromacs-2019.1/build/documentation /build/gromacs-2019.1/build/documentation/docs /build/gromacs-2019.1/build/documentation/docs/CMakeFiles/webpage.dir/DependInfo.cmake --color= Scanning dependencies of target webpage make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/make -f docs/CMakeFiles/webpage.dir/build.make docs/CMakeFiles/webpage.dir/build make[4]: Entering directory '/build/gromacs-2019.1/build/documentation' cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E echo "webpage was built, but with the following limitations:" webpage was built, but with the following limitations: cd /build/gromacs-2019.1/build/documentation/docs && /usr/bin/cmake -E echo " - Reference PDF manual was not built, so links to it do not work" - Reference PDF manual was not built, so links to it do not work make[4]: Leaving directory '/build/gromacs-2019.1/build/documentation' [100%] Built target webpage make[3]: Leaving directory '/build/gromacs-2019.1/build/documentation' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/documentation/CMakeFiles 0 make[2]: Leaving directory '/build/gromacs-2019.1/build/documentation' make[1]: Leaving directory '/build/gromacs-2019.1/build/documentation' dh_testdir dh_testroot dh_prep -pgromacs dh_installdirs -pgromacs /usr/bin/make -j8 -C build/basic install DESTDIR=/build/gromacs-2019.1/debian/gromacs make[1]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles /build/gromacs-2019.1/build/basic/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /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/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs /build/gromacs-2019.1/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/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 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'/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic /build/gromacs-2019.1/build/basic/src/gromacs /build/gromacs-2019.1/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic' cd /build/gromacs-2019.1/build/basic && /usr/bin/cmake 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast -Wl,-z,relro -Wl,-z,now -Wl,--as-needed CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx -Wl,-rpath,/build/gromacs-2019.1/build/basic/lib: ../../lib/libgromacs.so.4.0.0 -fopenmp /usr/lib/aarch64-linux-gnu/libX11.so -lm make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target template make[3]: Leaving directory '/build/gromacs-2019.1/build/basic' [100%] Built target gmx make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/basic' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/basic' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-wheel.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-anadock.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sigeps.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-x2top.1 -- Installing: 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Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-select.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-clustsize.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-hbond.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rdf.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/urea.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4pew.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/tip5p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/dna.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/atomtypes.atp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/rna.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amberGS.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/co-shift.dat -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/tip4p.gro -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/atom_nom.tbl -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffG53a6.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/vdw-msms.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/cmap.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tips3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/lipids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/tip5p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/atomtypes.atp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/dna.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnanonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnabonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/rna.arn -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/charmm27.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffG53a5.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/nsfactor.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/dppc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ff_dum.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tmcl.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/popc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/atomtypes.atp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.hdb -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/tip5p.gro -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/surface.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ps.m2p -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Installing: 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-- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/atommass.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/electroneg.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/residues.xml -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/defselection.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/sw.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/urea.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/tip4pew.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.hdb -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffoplsaa.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/xlateat.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ions.itp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/random.dat -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/README -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/template.cpp -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/Makefile.pkg -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.csh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/version.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs.so.4.0.0 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs.so.4 -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs.so.4.0.0" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs.so -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/ishift.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/pbc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/rmpbc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/exponentialdistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/gammadistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/normaldistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/seed.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/tabulatednormaldistribution.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/threefry.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformintdistribution.h -- Installing: 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/build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/basedefinitions.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/baseversion.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/classhelpers.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/cstringutil.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/current_function.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/datafilefinder.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/errorcodes.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/exceptions.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fatalerror.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/flags.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fileptr.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/futil.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/gmxassert.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/init.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/programcontext.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/real.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/smalloc.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/stringutil.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/unique_cptr.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/confio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/enxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/filetypes.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/gmxfio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/matio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/mtxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/oenv.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/pdbio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/rgb.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/tpxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trrio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trxio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xdr_datatype.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xtcio.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xvgr.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/compat/make_unique.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gmxana/gstat.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/abstractdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/analysisdata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/arraydata.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/dataframe.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/datamodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/average.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/displacement.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/histogram.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/lifetime.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/plot.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/nbsearch.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/indexutil.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/position.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectioncollection.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionenums.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoption.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionbehavior.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionmanager.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/bin/gmx" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion-gmx.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/basic' /usr/bin/make -j8 -C build/basic-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs make[1]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles /build/gromacs-2019.1/build/basic-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/depend /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-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/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= /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/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color= [ 0%] Built target lmfit_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests /build/gromacs-2019.1/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/view_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build [ 1%] Built target view_objlib [ 2%] Built target tng_io_obj make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/mdrun/tests/CMakeFiles/mdrun_test_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 7%] Built target libgromacs_external [ 8%] Built target mdrun_objlib [ 24%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend [ 24%] Built target mdrun_test_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/gromacs /build/gromacs-2019.1/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/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/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target libgromacs /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/share/template /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/share/template /build/gromacs-2019.1/build/basic-dp/share/template/CMakeFiles/template.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' cd /build/gromacs-2019.1/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/basic-dp /build/gromacs-2019.1/build/basic-dp/src/programs /build/gromacs-2019.1/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/gmx.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[3]: Nothing to be done for 'share/template/CMakeFiles/template.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' [ 98%] Built target gmx [100%] Built target template make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/basic-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/basic-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-densorder.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmtraj.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-spatial.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-do_dssp.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-wheel.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-anadock.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-angle.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dump.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sigeps.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sham.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-x2top.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-filter.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-order.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-eneconv.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rmsf.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-confrms.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-spol.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-bar.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-enemat.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-chi.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-distance.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rmsdist.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-densmap.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-covar.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dipoles.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-select.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mk_angndx.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-clustsize.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-hbond.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sasa.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rdf.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-traj.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pdb2gmx.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mindist.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-view.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-make_ndx.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-energy.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-bundle.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-insert-molecules.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genrestr.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-principal.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-awh.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-analyze.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjcat.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dos.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-anaeig.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genconf.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-polystat.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-density.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-potential.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-mdmat.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-help.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-saltbr.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rama.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-cluster.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-vanhove.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-sans.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trajectory.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-saxs.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rotacf.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-rotmat.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-gyrate.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-h2order.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-convert-tpr.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pme_error.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-trjorder.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-helix.1 -- Up-to-date: 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Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-check.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-gangle.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-genion.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dyecoupl.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-pairdist.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-velacc.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-current.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-nmr.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-dielectric.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-freevolume.1 -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/man/man1/gmx-tcaf.1 -- Up-to-date: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos54a7.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ff_dum.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/atomname2type.n2t -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos53a5.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/tip5p.gro -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/surface.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ps.m2p -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol216.gro -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ff_dum.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/methanol.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a1.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/atommass.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/electroneg.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/residues.xml -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/defselection.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/sw.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ff_dum.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/gromos43a2.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/export.dlg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/urea.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4pew.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/tip5p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/rna.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/dna.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber03.ff/aminoacids.hdb -- Up-to-date: 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Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/spc216.gro -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ha-shift.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/elements.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-10.xvg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/dna.rtp -- Up-to-date: 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/build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/rna.arn -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/amber99sb-ildn.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/table6-9.xvg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/flexwat-ferguson.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/edissoc.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ffoplsaa.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spc.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip3p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/watermodels.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5pe.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/forcefield.doc -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ethanol.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4pew.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/1propanol.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip4p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/tip5p.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomtypes.atp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.vsd -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/spce.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/methanol.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ffnonbonded.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/atomname2type.n2t -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/oplsaa.ff/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/xlateat.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/ions.itp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top/random.dat -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/CMakeLists.txt -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/README -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/template.cpp -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/Makefile.pkg -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template/cmake/FindGROMACS.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.zsh -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC.csh -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/version.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs_d.so.4.0.0 -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs_d.so.4 -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs_d.so.4.0.0" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/libgromacs_d.so -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/pkgconfig/libgromacs_d.pc -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/libgromacs-release.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config.cmake -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/share/cmake/gromacs_d/gromacs_d-config-version.cmake -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdlib/simulationsignal.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinehelpwriter.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineinit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlinemodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineoptionsmodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineparser.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/cmdlineprogramcontext.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/filenm.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/pargs.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/commandline/viewit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fft/fft.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gpu_utils/hostallocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/eigensolver.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/matrix.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/linearalgebra/sparsematrix.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/3dtransforms.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/arrayrefwithpadding.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/do_fit.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/functions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/gmxcomplex.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/units.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/utilities.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vec.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/vectypes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/math/paddedvector.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/inputrec.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/mdatom.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/md_enums.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/mdtypes/state.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/abstractsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/basicoptions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/filenameoptionmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionsbehavior.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainer.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ioptionscontainerwithsections.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/isectionstorage.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/ivaluestore.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionfiletype.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionflags.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/options.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/optionsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/repeatingsection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/timeunitmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/options/valuestore.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/ishift.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/pbc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/pbcutil/rmpbc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/exponentialdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/gammadistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/normaldistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/seed.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/tabulatednormaldistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/threefry.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformintdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/random/uniformrealdistribution.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/restraint/restraintpotential.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/wallcycle.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/timing/walltime_accounting.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atomprop.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/atoms.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/block.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/forcefieldparameters.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/idef.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/ifunc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/index.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/mtop_util.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/symtab.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/topology/topology.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectory/energyframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectory/trajectoryframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/alignedallocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/allocator.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/arrayref.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/arraysize.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/basedefinitions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/baseversion.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/classhelpers.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/cstringutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/current_function.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/datafilefinder.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/errorcodes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/exceptions.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fatalerror.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/flags.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/fileptr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/futil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/gmxassert.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/init.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/programcontext.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/real.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/smalloc.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/stringutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/utility/unique_cptr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/confio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/enxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/filetypes.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/gmxfio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/matio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/mtxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/oenv.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/pdbio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/rgb.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/tpxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trrio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/trxio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xdr_datatype.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xtcio.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/fileio/xvgr.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/compat/make_unique.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/gmxana/gstat.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/abstractdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/analysisdata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/arraydata.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/dataframe.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/datamodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/average.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/displacement.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/histogram.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/lifetime.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/analysisdata/modules/plot.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/nbsearch.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/indexutil.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/position.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectioncollection.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionenums.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoption.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionbehavior.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/selection/selectionoptionmanager.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysismodule.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/analysissettings.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/include/gromacs/trajectoryanalysis/topologyinformation.h -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin -- Up-to-date: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion.bash -- Installing: /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx-completion-gmx_d.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/basic-dp' dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1 # gmx(1) -> gmx_d(1) dh_link -pgromacs -pgromacs-data # temporary as of 2019-beta2 and removal of CMAKE_SKIP_RPATH chrpath -d /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx_d dh_testdir dh_testroot dh_prep -pgromacs-mpich dh_installdirs -pgromacs-mpich /usr/bin/make -j8 -C build/mpich install DESTDIR=/build/gromacs-2019.1/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles /build/gromacs-2019.1/build/mpich/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /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/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build [ 0%] Built target mdrun_objlib make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 2%] Built target tng_io_obj make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 3%] Built target libgromacs_external [ 5%] Built target lmfit_objlib [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/gromacs /build/gromacs-2019.1/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' cd /build/gromacs-2019.1/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich /build/gromacs-2019.1/build/mpich/src/programs /build/gromacs-2019.1/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/mpich' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi.mpich" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich' /usr/bin/make -j8 -C build/mpich-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs-mpich make[1]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles /build/gromacs-2019.1/build/mpich-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-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/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 0%] Built target mdrun_objlib [ 22%] Built target libgromacs_generated [ 23%] Built target lmfit_objlib [ 26%] Built target tng_io_obj [ 27%] Built target libgromacs_external /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/gromacs /build/gromacs-2019.1/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' cd /build/gromacs-2019.1/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/mpich-dp /build/gromacs-2019.1/build/mpich-dp/src/programs /build/gromacs-2019.1/build/mpich-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/mpich-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/mpich-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi_d.mpich" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/mpich-dp' chmod 644 /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion* mv /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi.mpich.bash /build/gromacs-2019.1/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi.mpich mv /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/gmx-completion-mdrun_mpi_d.mpich.bash /build/gromacs-2019.1/debian/gromacs-mpich/usr/share/bash-completion/completions/mdrun_mpi_d.mpich # temporary as of 2019-beta2 chrpath -d /build/gromacs-2019.1/debian/gromacs-mpich/usr/bin/mdrun_mpi* dh_installman -pgromacs-mpich debian/man/mdrun_mpi.mpich.1 dh_link -pgromacs-mpich usr/share/man/man1/mdrun_mpi.mpich.1.gz usr/share/man/man1/mdrun_mpi_d.mpich.1.gz dh_lintian -pgromacs-mpich dh_testdir dh_testroot dh_prep -pgromacs-openmpi dh_installdirs -pgromacs-openmpi /usr/bin/make -j8 -C build/openmpi install DESTDIR=/build/gromacs-2019.1/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles /build/gromacs-2019.1/build/openmpi/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build [ 1%] Built target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 3%] Built target tng_io_obj [ 5%] Built target libgromacs_external [ 5%] Built target mdrun_objlib [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/gromacs /build/gromacs-2019.1/build/openmpi/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' cd /build/gromacs-2019.1/build/openmpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi /build/gromacs-2019.1/build/openmpi/src/programs /build/gromacs-2019.1/build/openmpi/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi.openmpi" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi' /usr/bin/make -j8 -C build/openmpi-dp install DESTDIR=/build/gromacs-2019.1/debian/gromacs-openmpi make[1]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -S/build/gromacs-2019.1 -B/build/gromacs-2019.1/build/openmpi-dp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.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/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color= /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/depend cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color= /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_external.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs_generated.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/programs /build/gromacs-2019.1/build/openmpi-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_external.dir/build.make src/gromacs/CMakeFiles/libgromacs_external.dir/build make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_external.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-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/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 1%] Built target libgromacs_external [ 2%] Built target mdrun_objlib [ 5%] Built target tng_io_obj [ 5%] Built target lmfit_objlib make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs_generated.dir/build.make src/gromacs/CMakeFiles/libgromacs_generated.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs_generated.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 27%] Built target libgromacs_generated /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/gromacs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/gromacs /build/gromacs-2019.1/build/openmpi-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [ 98%] Built target libgromacs /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' cd /build/gromacs-2019.1/build/openmpi-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/gromacs-2019.1 /build/gromacs-2019.1/src/programs /build/gromacs-2019.1/build/openmpi-dp /build/gromacs-2019.1/build/openmpi-dp/src/programs /build/gromacs-2019.1/build/openmpi-dp/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build make[3]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[3]: Nothing to be done for 'src/programs/CMakeFiles/mdrun.dir/build'. make[3]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' [100%] Built target mdrun make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' /usr/bin/cmake -E cmake_progress_start /build/gromacs-2019.1/build/openmpi-dp/CMakeFiles 0 /usr/bin/make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/gromacs-2019.1/build/openmpi-dp' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi -- Set runtime path of "/build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi_d.openmpi" to "$ORIGIN/../lib/aarch64-linux-gnu" -- Installing: /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash make[1]: Leaving directory '/build/gromacs-2019.1/build/openmpi-dp' chmod 644 /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion* mv /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi.openmpi.bash /build/gromacs-2019.1/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi.openmpi mv /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/gmx-completion-mdrun_mpi_d.openmpi.bash /build/gromacs-2019.1/debian/gromacs-openmpi/usr/share/bash-completion/completions/mdrun_mpi_d.openmpi # Force-disable RUNPATH - see # and lintian tag binary-or-shlib-defines-rpath in versions >= 2.5.50 chrpath -d /build/gromacs-2019.1/debian/gromacs-openmpi/usr/bin/mdrun_mpi* dh_installman -pgromacs-openmpi debian/man/mdrun_mpi.openmpi.1 dh_link -pgromacs-openmpi usr/share/man/man1/mdrun_mpi.openmpi.1.gz usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz dh_lintian -pgromacs-openmpi dh_testdir dh_testroot dh_prep -pgromacs-data -plibgromacs-dev dh_installdirs -pgromacs-data mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/top \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/gromacs mv /build/gromacs-2019.1/debian/gromacs/usr/share/man \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/man # some of the default installation directories for documentation and # example shell scripts are not FHS-friendly; move them appropriately cat /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx*.bash > \ /build/gromacs-2019.1/debian/gromacs-data/usr/share/bash-completion/completions/gmx rm -f /build/gromacs-2019.1/debian/gromacs/usr/bin/GMXRC* /build/gromacs-2019.1/debian/gromacs/usr/bin/gmx*.bash # symlinks, primarily for /usr/share/doc/{gromacs,libgromacs*} -> gromacs-data dh_link -pgromacs-data # rename a pair of Perl scripts to drop the .pl extension (Policy 10.4) mv /build/gromacs-2019.1/debian/gromacs/usr/bin/demux.pl /build/gromacs-2019.1/debian/gromacs/usr/bin/demux mv /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx.pl /build/gromacs-2019.1/debian/gromacs/usr/bin/xplor2gmx mkdir -p /build/gromacs-2019.1/debian/libgromacs4/usr/lib/aarch64-linux-gnu mv /build/gromacs-2019.1/debian/gromacs/usr/lib/*/*.so.* /build/gromacs-2019.1/debian/libgromacs4/usr/lib/aarch64-linux-gnu/ dh_installdirs -plibgromacs-dev mv /build/gromacs-2019.1/debian/gromacs/usr/include /build/gromacs-2019.1/debian/libgromacs-dev/usr/include # catch normal libraries plus all applicable MPI variants mkdir -p /build/gromacs-2019.1/debian/libgromacs-dev/usr/lib/aarch64-linux-gnu mv /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/*.so \ /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu/pkgconfig \ /build/gromacs-2019.1/debian/libgromacs-dev/usr/lib/aarch64-linux-gnu/ rmdir /build/gromacs-2019.1/debian/gromacs/usr/lib/aarch64-linux-gnu /build/gromacs-2019.1/debian/gromacs/usr/lib mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/template /build/gromacs-2019.1/debian/libgromacs-dev/usr/share/gromacs/template # remaining documentation catch-all mv /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs/* /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs rmdir /build/gromacs-2019.1/debian/gromacs/usr/share/gromacs # what are you doing here? mv /build/gromacs-2019.1/debian/gromacs/usr/share/cmake /build/gromacs-2019.1/debian/libgromacs-dev/usr/share/gromacs/ dh_lintian -pgromacs -pgromacs-data -plibgromacs4 dh_testdir dh_testroot dh_install -pgromacs-data rdfind -outputname /dev/null -makesymlinks true /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/ Now scanning "/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc", found 23772 files. Now have 23772 files in total. Removed 0 files due to nonunique device and inode. Total size is 187255187 bytes or 179 MiB Removed 5899 files due to unique sizes from list.17873 files left. Now eliminating candidates based on first bytes:removed 5250 files from list.12623 files left. Now eliminating candidates based on last bytes:removed 1350 files from list.11273 files left. Now eliminating candidates based on sha1 checksum:removed 1645 files from list.9628 files left. It seems like you have 9628 files that are not unique Totally, 16 MiB can be reduced. Now making results file /dev/null Now making symbolic links. creating Making 5601 links. symlinks -r -s -c /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/ dangling: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs-data/COPYING -> copyright absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/jquery.js changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/jquery.js -> ../html-full/jquery.js absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/trajectoryanalysis_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/trajectoryanalysis_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/trajectoryanalysis_8h__incl.svg -> ../html-full/trajectoryanalysis_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/template_8cpp__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/template_8cpp__incl.svg -> ../html-full/template_8cpp__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/random_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/random_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/random_8h__incl.svg -> ../html-full/random_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/position_8h.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/position_8h.xhtml -> ../html-lib/position_8h.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64General.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64General.xhtml -> ../html-full/classgmx_1_1ThreeFry2x64General.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysisdata_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysisdata_8h__incl.svg -> ../html-full/analysisdata_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selection_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selection_8h__incl.svg -> ../html-full/selection_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64Fast.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64Fast.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1ThreeFry2x64.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ThreeFry2x64.xhtml -> ../html-lib/classgmx_1_1ThreeFry2x64.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/state_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/state_8h__incl.svg -> ../html-full/state_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TabulatedNormalDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TabulatedNormalDistribution.xhtml -> ../html-full/classgmx_1_1TabulatedNormalDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataPointSetRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataPointSetRef.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/options_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/options_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/options_8h__incl.svg -> ../html-full/options_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataFrameRef.xhtml -> ../html-lib/classgmx_1_1AnalysisDataFrameRef.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mdatoms.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structt__mdatoms.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/structt__mdatoms.xhtml -> ../html-full/structt__mdatoms.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/commandline_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/commandline_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/commandline_8h__incl.svg -> ../html-full/commandline_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1TextLineWrapper.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1TextLineWrapper.xhtml -> ../html-lib/classgmx_1_1TextLineWrapper.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/hostallocator_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/hostallocator_8h__incl.svg -> ../html-full/hostallocator_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/doxygen.css changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/doxygen.css -> ../html-full/doxygen.css absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BasicVector.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BasicVector.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1BasicVector.xhtml -> ../html-full/classgmx_1_1BasicVector.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/repeatingsection_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/repeatingsection_8h__incl.svg -> ../html-full/repeatingsection_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformIntDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformIntDistribution.xhtml -> ../html-full/classgmx_1_1UniformIntDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1GammaDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1GammaDistribution.xhtml -> ../html-full/classgmx_1_1GammaDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1UniformRealDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1UniformRealDistribution.xhtml -> ../html-full/classgmx_1_1UniformRealDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1NormalDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1NormalDistribution.xhtml -> ../html-full/classgmx_1_1NormalDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ExponentialDistribution.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1ExponentialDistribution.xhtml -> ../html-full/classgmx_1_1ExponentialDistribution.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoption_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoption_8h__incl.svg -> ../html-full/selectionoption_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/cmdlinerunner_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/cmdlinerunner_8h__incl.svg -> ../html-full/cmdlinerunner_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_6.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/msc_inline_mscgraph_6.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/msc_inline_mscgraph_6.svg -> ../html-full/msc_inline_mscgraph_6.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000031_000013.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/dir_000031_000013.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/dir_000031_000013.xhtml -> ../html-lib/dir_000031_000013.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/threefry_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/threefry_8h__incl.svg -> ../html-full/threefry_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysismodule_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/analysismodule_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/analysismodule_8h__incl.svg -> ../html-full/analysismodule_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/basicoptions_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/basicoptions_8h__incl.svg -> ../html-full/basicoptions_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectioncollection_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectioncollection_8h__incl.svg -> ../html-full/selectioncollection_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/average_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/average_8h__incl.svg -> ../html-full/average_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1AnalysisDataValue.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1AnalysisDataValue.xhtml -> ../html-full/classgmx_1_1AnalysisDataValue.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/lifetime_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/lifetime_8h__incl.svg -> ../html-full/lifetime_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.svg -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/histogram_8h__incl.svg changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/histogram_8h__incl.svg -> ../html-full/histogram_8h__incl.svg absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-lib/classgmx_1_1SelectionOptionBehavior.xhtml changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1SelectionOptionBehavior.xhtml -> ../html-lib/classgmx_1_1SelectionOptionBehavior.xhtml absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1PaddedVector-members.xhtml -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1PaddedVector-members.xhtml changed: 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-> ../html-full/classgmx_1_1AnalysisDataDisplacementModule__inherit__graph.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__inherit__graph.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/classgmx_1_1RepeatingOptionSection__inherit__graph.md5 -> ../html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.md5 absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.md5 -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/selectionoptionmanager_8h__incl.md5 changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-user/selectionoptionmanager_8h__incl.md5 -> 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__inherit__graph.map -> classanonymous__namespace_02legacymodules_8cpp_03_1_1ObsoleteToolModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02freevolume_8cpp_03_1_1FreeVolume__inherit__graph.map -> 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classgmx_1_1anonymous__namespace_02cmdlinehelpwriter_8cpp_03_1_1OptionsFilter__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1test_1_1HostAllocatorTest__inherit__graph.map -> structgmx_1_1test_1_1HostAllocatorTest__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1analysismodules_1_1anonymous__namespace_02sasa_8cpp_03_1_1Sasa__coll__graph.map changed: 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSectionStorage__inherit__graph.map -> classgmx_1_1RepeatingOptionSectionStorage__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1ThreeFry2x64__inherit__graph.map -> classgmx_1_1ThreeFry2x64__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1MockOptionsModule__inherit__graph.map -> classgmx_1_1test_1_1MockOptionsModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1CommandLineModuleManagerTestBase__inherit__graph.map -> classgmx_1_1test_1_1CommandLineModuleManagerTestBase__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1TestFileOutputRedirector__inherit__graph.map -> classgmx_1_1test_1_1TestFileOutputRedirector__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionStorage__coll__graph.map changed: 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineProgramContext__inherit__graph.map -> classgmx_1_1CommandLineProgramContext__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RepeatingOptionSection__inherit__graph.map -> classgmx_1_1RepeatingOptionSection__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1EnumIndexStore__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1EnumIndexStore__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1internal_1_1EnumIndexStore__inherit__graph.map -> classgmx_1_1internal_1_1EnumIndexStore__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1FilteringExactTextMatch__coll__graph.map changed: 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changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1CommandLineHelpModule__inherit__graph.map -> classgmx_1_1CommandLineHelpModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SelectionFileOptionInfo__inherit__graph.map -> classgmx_1_1SelectionFileOptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1OpenClTraits_3_01cl__program_01_4__inherit__graph.map -> 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classgmx_1_1FileNameOptionInfo__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1SimulationInstabilityError__inherit__graph.map -> classgmx_1_1SimulationInstabilityError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1BooleanOptionInfo__inherit__graph.map -> 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/build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/structgmx_1_1Constraints_1_1CreationHelper__inherit__graph.map -> structgmx_1_1Constraints_1_1CreationHelper__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1FileIOError__inherit__graph.map -> classgmx_1_1FileIOError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RestraintMDModule__inherit__graph.map -> classgmx_1_1RestraintMDModule__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1RangeError__inherit__graph.map -> classgmx_1_1RangeError__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1test_1_1Simd4Test__inherit__graph.map -> classgmx_1_1test_1_1Simd4Test__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StandardInputStream__inherit__graph.map -> classgmx_1_1StandardInputStream__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringOutputStream__inherit__graph.map -> classgmx_1_1StringOutputStream__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1StringInputStream__inherit__graph.map -> classgmx_1_1StringInputStream__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextOutputFile__inherit__graph.map -> classgmx_1_1TextOutputFile__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.map -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__coll__graph.map changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/classgmx_1_1TextInputFile__inherit__graph.map -> classgmx_1_1TextInputFile__coll__graph.map absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_1c.js changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/functions_1b.js -> all_1c.js absolute: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/all_0.js changed: /build/gromacs-2019.1/debian/gromacs-data/usr/share/doc/gromacs/html/doxygen/html-full/search/related_0.js -> all_0.js dh_testdir dh_testroot dh_installchangelogs -i dh_installdocs -pgromacs-data dh_compress -i -X.pdf dh_fixperms -i dh_installdeb -i dh_gencontrol -i dh_md5sums -i dh_builddeb -i dpkg-deb: building package 'gromacs-data' in '../gromacs-data_2019.1-1_all.deb'. dh_testdir -a dh_testroot -a dh_installchangelogs -a dh_installdocs -a dh_strip -A dh_compress -a dh_fixperms -a dh_makeshlibs -a dh_shlibdeps -plibgromacs4 -L libgromacs4 -l debian/libgromacs4/usr/lib dh_shlibdeps -pgromacs -L libgromacs4 -l debian/libgromacs4/usr/lib:debian/gromacs/usr/lib dh_shlibdeps -pgromacs-mpich -L gromacs-mpich -l debian/gromacs-mpich/usr/lib dh_shlibdeps -pgromacs-openmpi -L gromacs-openmpi -l debian/gromacs-openmpi/usr/lib dh_gencontrol -a dpkg-gencontrol: warning: Depends field of package libgromacs-dev: substitution variable ${shlibs:Depends} used, but is not defined dh_installdeb -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'gromacs' in '../gromacs_2019.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-mpich-dbgsym' in '../gromacs-mpich-dbgsym_2019.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs4' in '../libgromacs4_2019.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-openmpi-dbgsym' in '../gromacs-openmpi-dbgsym_2019.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs-dev' in '../libgromacs-dev_2019.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-dbgsym' in '../gromacs-dbgsym_2019.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-mpich' in '../gromacs-mpich_2019.1-1_arm64.deb'. dpkg-deb: building package 'gromacs-openmpi' in '../gromacs-openmpi_2019.1-1_arm64.deb'. dpkg-deb: building package 'libgromacs4-dbgsym' in '../libgromacs4-dbgsym_2019.1-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gromacs_2019.1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2947 and its subdirectories I: Current time: Sun Mar 13 14:04:26 -12 2022 I: pbuilder-time-stamp: 1647223466